Updating workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 from 0.2.7 to 0.2.8 #514

gxydevbot · 2024-08-22T15:45:52Z

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1

The workflow release number has been updated from 0.2.7 to 0.2.8.

gxydevbot · 2024-08-26T04:24:48Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-02T04:28:33Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-09T04:26:32Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-16T04:25:14Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-23T04:27:59Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-23T14:04:58Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-23T15:14:53Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input GFA:
- step_state: scheduled
Step 2: Haplotype:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "$&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "hap1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 12: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpvdvotu4c/files/9/5/e/dataset_95e5807f-f479-4ca1-8171-06020524adca.dat'  -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 84
Total scaffold length: 1982895
Average scaffold length: 23605.89
Scaffold N50: 20934
Scaffold auN: 33899.67
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 84
Total contig length: 1982895
Average contig length: 23605.89
Contig N50: 20934
Contig auN: 33899.67
Contig L50: 30
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 606458:383991:386001:606445
GC content %: 38.83
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 84
# edges: 4
Average degree: 0.05
# connected components: 1
Largest connected component length: 94650
# dead ends: 165
# disconnected components: 81
Total length disconnected components: 1888245
# separated components: 82
# bubbles: 0
# circular segments: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpvdvotu4c/files/f/b/8/dataset_fb89d026-ef8e-4ad9-8c41-d71f16980b3e.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpvdvotu4c/files/2/3/c/dataset_23cc1cd1-97f3-451a-8a76-4044b392dcb9.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpvdvotu4c/job_working_directory/000/8/outputs/dataset_3f5b00fe-4d07-48c0-a779-e4d83afb9127.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 123125044
ref seq len = 3965790
binary seq ticks = 68161474
build suffix-array ticks = 589914043
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 172766669
Total time taken: 0.3995
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 3041008
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000037, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000037 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000053, nseq: 100108
	[0000][ M::kt_pipeline] read 100108 sequences (10000053 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 5.050 CPU sec, 5.054 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000072, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000072 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100108 reads in 5.346 CPU sec, 5.424 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000203, nseq: 100132
	[0000][ M::kt_pipeline] read 100132 sequences (10000203 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 5.142 CPU sec, 5.220 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000073, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000073 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100132 reads in 5.184 CPU sec, 5.263 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000141, nseq: 100166
	[0000][ M::kt_pipeline] read 100166 sequences (10000141 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 5.120 CPU sec, 5.189 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000104, nseq: 118598
	[0000][ M::kt_pipeline] read 118598 sequences (10000104 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100166 reads in 5.056 CPU sec, 5.125 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000109, nseq: 151884
	[0000][ M::kt_pipeline] read 151884 sequences (10000109 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118598 reads in 5.054 CPU sec, 5.131 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000126, nseq: 151908
	[0000][ M::kt_pipeline] read 151908 sequences (10000126 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151884 reads in 4.736 CPU sec, 4.820 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151908 reads in 5.023 CPU sec, 5.120 real sec
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000007, nseq: 151868
	[0000][ M::kt_pipeline] read 151868 sequences (10000007 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 4.929 CPU sec, 5.024 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000077, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000077 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151868 reads in 4.897 CPU sec, 4.989 real sec
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000024, nseq: 127818
	[0000][ M::kt_pipeline] read 127818 sequences (10000024 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 4.841 CPU sec, 4.939 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000071, nseq: 98956
	[0000][ M::kt_pipeline] read 98956 sequences (10000071 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127818 reads in 6.473 CPU sec, 6.575 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000004, nseq: 145156
	[0000][ M::kt_pipeline] read 145156 sequences (10000004 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98956 reads in 8.284 CPU sec, 8.370 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3496096, nseq: 53016
	[0000][ M::kt_pipeline] read 53016 sequences (3496096 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145156 reads in 7.321 CPU sec, 7.404 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 53016 reads in 2.676 CPU sec, 2.777 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.628000 MHz
Runtime profile:

	Time taken for main_mem function: 86.65 sec

	IO times (sec) :
	Reading IO time (reads) avg: 5.14, (5.14, 5.14)
	Writing IO time (SAM) avg: 3.93, (3.93, 3.93)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.00, (0.00, 0.00)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 86.64
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 86.42, (86.42, 86.42)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 8.03, (8.03, 8.03)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 78.39, (78.39, 78.39)
		SMEM compute avg: 25.07, (25.07, 25.07)
		SAL compute avg: 16.34, (16.34, 16.34)
				MEM_SA avg: 7.87, (7.87, 7.87)

		BSW time, avg: 32.07, (32.07, 32.07)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[3041008] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 2, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 7, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpvdvotu4c/files/f/b/8/dataset_fb89d026-ef8e-4ad9-8c41-d71f16980b3e.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpvdvotu4c/files/8/9/a/dataset_89a3de3f-59a2-44b7-bde0-edb0b2676323.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpvdvotu4c/job_working_directory/000/9/outputs/dataset_2b6e1e1c-50b0-4665-8527-761d5c1e3a72.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 125180692
ref seq len = 3965790
binary seq ticks = 67606157
build suffix-array ticks = 638860427
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 172476692
Total time taken: 0.4209
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 3041008
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000036, nseq: 100212
	[0000][ M::kt_pipeline] read 100212 sequences (10000036 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000140, nseq: 100074
	[0000][ M::kt_pipeline] read 100074 sequences (10000140 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100212 reads in 5.025 CPU sec, 5.025 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000066, nseq: 100106
	[0000][ M::kt_pipeline] read 100106 sequences (10000066 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100074 reads in 5.142 CPU sec, 5.229 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000070, nseq: 100180
	[0000][ M::kt_pipeline] read 100180 sequences (10000070 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100106 reads in 5.281 CPU sec, 5.367 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000000, nseq: 100202
	[0000][ M::kt_pipeline] read 100202 sequences (10000000 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100180 reads in 5.056 CPU sec, 5.140 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000132, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000132 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100202 reads in 5.033 CPU sec, 5.110 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 118588
	[0000][ M::kt_pipeline] read 118588 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 5.190 CPU sec, 5.279 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000125, nseq: 151900
	[0000][ M::kt_pipeline] read 151900 sequences (10000125 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118588 reads in 4.977 CPU sec, 5.065 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000005, nseq: 151874
	[0000][ M::kt_pipeline] read 151874 sequences (10000005 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151900 reads in 4.795 CPU sec, 4.881 real sec
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151904
	[0000][ M::kt_pipeline] read 151904 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151874 reads in 4.771 CPU sec, 4.867 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151896
	[0000][ M::kt_pipeline] read 151896 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151904 reads in 4.746 CPU sec, 4.847 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000130, nseq: 151906
	[0000][ M::kt_pipeline] read 151906 sequences (10000130 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151896 reads in 4.824 CPU sec, 4.927 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 127808
	[0000][ M::kt_pipeline] read 127808 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151906 reads in 4.841 CPU sec, 4.945 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000028, nseq: 98948
	[0000][ M::kt_pipeline] read 98948 sequences (10000028 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127808 reads in 6.263 CPU sec, 6.367 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000026, nseq: 145218
	[0000][ M::kt_pipeline] read 145218 sequences (10000026 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98948 reads in 8.380 CPU sec, 8.470 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3489223, nseq: 52906
	[0000][ M::kt_pipeline] read 52906 sequences (3489223 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145218 reads in 7.158 CPU sec, 7.243 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 52906 reads in 2.646 CPU sec, 2.750 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.557268 MHz
Runtime profile:

	Time taken for main_mem function: 85.74 sec

	IO times (sec) :
	Reading IO time (reads) avg: 5.32, (5.32, 5.32)
	Writing IO time (SAM) avg: 4.01, (4.01, 4.01)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.00, (0.00, 0.00)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 85.73
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 85.50, (85.50, 85.50)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 7.82, (7.82, 7.82)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 77.68, (77.68, 77.68)
		SMEM compute avg: 25.14, (25.14, 25.14)
		SAL compute avg: 16.86, (16.86, 16.86)
				MEM_SA avg: 8.53, (8.53, 8.53)

		BSW time, avg: 31.18, (31.18, 31.18)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[3041008] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 3, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 7, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpvdvotu4c/files/3/f/5/dataset_3f5b00fe-4d07-48c0-a779-e4d83afb9127.dat' 'forward_input.bam' && ln -s '/tmp/tmpvdvotu4c/files/2/b/6/dataset_2b6e1e1c-50b0-4665-8527-761d5c1e3a72.dat' 'reverse_input.bam' && bellerophon --forward forward_input.bam --reverse reverse_input.bam --quality 20 --output 'merged_out.bam' --threads ${GALAXY_SLOTS:-1} && samtools sort --no-PG -O BAM -o '/tmp/tmpvdvotu4c/job_working_directory/000/10/outputs/dataset_ca1ee6de-2d54-43a5-8c89-325e6011c8a7.dat' -@ ${GALAXY_SLOTS:-1} merged_out.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmpvdvotu4c/files/c/a/1/dataset_ca1ee6de-2d54-43a5-8c89-325e6011c8a7.dat' | PretextMap -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 84 sequences, sorted by length, descending. Filtering by minimum mapping quality 10

                                                                                
[PretextMap status] :: 10.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 10.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 15.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 20.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 25.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 30.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 35.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 40.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 45.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 50.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 55.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 60.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 65.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 70.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 75.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 80.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 85.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 90.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 95.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 100.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 104.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 109.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 114.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 119.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 124.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 129.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 134.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 139.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 145.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 150.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 154.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 159.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 165.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 170.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 175.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 180.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 185.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 190.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 195.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 200.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 205.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 210.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 215.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 220.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 225.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 230.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 235.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 240.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 245.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 250.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 255.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 260.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 265.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 270.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 275.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 280.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 285.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 290.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 295.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 300.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 305.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 310.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 315.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 640.0 k reads processed, 320.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 650.0 k reads processed, 325.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 660.0 k reads processed, 330.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 670.0 k reads processed, 335.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 680.0 k reads processed, 340.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 690.0 k reads processed, 345.0 k read-pairs mapped
[PretextMap status] :: Creating MipMaps...
[PretextMap status] :: Equalising contrast...
[PretextMap status] :: Compressing textures...

[PretextMap status] ::   1/528 (0.19%) texture blocks written to disk
[PretextMap status] ::   2/528 (0.38%) texture blocks written to disk
[PretextMap status] ::   3/528 (0.57%) texture blocks written to disk
[PretextMap status] ::   4/528 (0.76%) texture blocks written to disk
[PretextMap status] ::   5/528 (0.95%) texture blocks written to disk
[PretextMap status] ::   6/528 (1.14%) texture blocks written to disk
[PretextMap status] ::   7/528 (1.33%) texture blocks written to disk
[PretextMap status] ::   8/528 (1.52%) texture blocks written to disk
[PretextMap status] ::   9/528 (1.70%) texture blocks written to disk
[PretextMap status] ::  10/528 (1.89%) texture blocks written to disk
[PretextMap status] ::  11/528 (2.08%) texture blocks written to disk
[PretextMap status] ::  12/528 (2.27%) texture blocks written to disk
[PretextMap status] ::  13/528 (2.46%) texture blocks written to disk
[PretextMap status] ::  14/528 (2.65%) texture blocks written to disk
[PretextMap status] ::  15/528 (2.84%) texture blocks written to disk
[PretextMap status] ::  16/528 (3.03%) texture blocks written to disk
[PretextMap status] ::  17/528 (3.22%) texture blocks written to disk
[PretextMap status] ::  18/528 (3.41%) texture blocks written to disk
[PretextMap status] ::  19/528 (3.60%) texture blocks written to disk
[PretextMap status] ::  20/528 (3.79%) texture blocks written to disk
[PretextMap status] ::  21/528 (3.98%) texture blocks written to disk
[PretextMap status] ::  22/528 (4.17%) texture blocks written to disk
[PretextMap status] ::  23/528 (4.36%) texture blocks written to disk
[PretextMap status] ::  24/528 (4.55%) texture blocks written to disk
[PretextMap status] ::  25/528 (4.73%) texture blocks written to disk
[PretextMap status] ::  26/528 (4.92%) texture blocks written to disk
[PretextMap status] ::  27/528 (5.11%) texture blocks written to disk
[PretextMap status] ::  28/528 (5.30%) texture blocks written to disk
[PretextMap status] ::  29/528 (5.49%) texture blocks written to disk
[PretextMap status] ::  30/528 (5.68%) texture blocks written to disk
[PretextMap status] ::  31/528 (5.87%) texture blocks written to disk
[PretextMap status] ::  32/528 (6.06%) texture blocks written to disk
[PretextMap status] ::  33/528 (6.25%) texture blocks written to disk
[PretextMap status] ::  34/528 (6.44%) texture blocks written to disk
[PretextMap status] ::  35/528 (6.63%) texture blocks written to disk
[PretextMap status] ::  36/528 (6.82%) texture blocks written to disk
[PretextMap status] ::  37/528 (7.01%) texture blocks written to disk
[PretextMap status] ::  38/528 (7.20%) texture blocks written to disk
[PretextMap status] ::  39/528 (7.39%) texture blocks written to disk
[PretextMap status] ::  40/528 (7.58%) texture blocks written to disk
[PretextMap status] ::  41/528 (7.77%) texture blocks written to disk
[PretextMap status] ::  42/528 (7.95%) texture blocks written to disk
[PretextMap status] ::  43/528 (8.14%) texture blocks written to disk
[PretextMap status] ::  44/528 (8.33%) texture blocks written to disk
[PretextMap status] ::  45/528 (8.52%) texture blocks written to disk
[PretextMap status] ::  46/528 (8.71%) texture blocks written to disk
[PretextMap status] ::  47/528 (8.90%) texture blocks written to disk
[PretextMap status] ::  48/528 (9.09%) texture blocks written to disk
[PretextMap status] ::  49/528 (9.28%) texture blocks written to disk
[PretextMap status] ::  50/528 (9.47%) texture blocks written to disk
[PretextMap status] ::  51/528 (9.66%) texture blocks written to disk
[PretextMap status] ::  52/528 (9.85%) texture blocks written to disk
[PretextMap status] ::  53/528 (10.04%) texture blocks written to disk
[PretextMap status] ::  54/528 (10.23%) texture blocks written to disk
[PretextMap status] ::  55/528 (10.42%) texture blocks written to disk
[PretextMap status] ::  56/528 (10.61%) texture blocks written to disk
[PretextMap status] ::  57/528 (10.80%) texture blocks written to disk
[PretextMap status] ::  58/528 (10.98%) texture blocks written to disk
[PretextMap status] ::  59/528 (11.17%) texture blocks written to disk
[PretextMap status] ::  60/528 (11.36%) texture blocks written to disk
[PretextMap status] ::  61/528 (11.55%) texture blocks written to disk
[PretextMap status] ::  62/528 (11.74%) texture blocks written to disk
[PretextMap status] ::  63/528 (11.93%) texture blocks written to disk
[PretextMap status] ::  64/528 (12.12%) texture blocks written to disk
[PretextMap status] ::  65/528 (12.31%) texture blocks written to disk
[PretextMap status] ::  66/528 (12.50%) texture blocks written to disk
[PretextMap status] ::  67/528 (12.69%) texture blocks written to disk
[PretextMap status] ::  68/528 (12.88%) texture blocks written to disk
[PretextMap status] ::  69/528 (13.07%) texture blocks written to disk
[PretextMap status] ::  70/528 (13.26%) texture blocks written to disk
[PretextMap status] ::  71/528 (13.45%) texture blocks written to disk
[PretextMap status] ::  72/528 (13.64%) texture blocks written to disk
[PretextMap status] ::  73/528 (13.83%) texture blocks written to disk
[PretextMap status] ::  74/528 (14.02%) texture blocks written to disk
[PretextMap status] ::  75/528 (14.20%) texture blocks written to disk
[PretextMap status] ::  76/528 (14.39%) texture blocks written to disk
[PretextMap status] ::  77/528 (14.58%) texture blocks written to disk
[PretextMap status] ::  78/528 (14.77%) textu
..
:: 298/528 (56.44%) texture blocks written to disk
[PretextMap status] :: 299/528 (56.63%) texture blocks written to disk
[PretextMap status] :: 300/528 (56.82%) texture blocks written to disk
[PretextMap status] :: 301/528 (57.01%) texture blocks written to disk
[PretextMap status] :: 302/528 (57.20%) texture blocks written to disk
[PretextMap status] :: 303/528 (57.39%) texture blocks written to disk
[PretextMap status] :: 304/528 (57.58%) texture blocks written to disk
[PretextMap status] :: 305/528 (57.77%) texture blocks written to disk
[PretextMap status] :: 306/528 (57.95%) texture blocks written to disk
[PretextMap status] :: 307/528 (58.14%) texture blocks written to disk
[PretextMap status] :: 308/528 (58.33%) texture blocks written to disk
[PretextMap status] :: 309/528 (58.52%) texture blocks written to disk
[PretextMap status] :: 310/528 (58.71%) texture blocks written to disk
[PretextMap status] :: 311/528 (58.90%) texture blocks written to disk
[PretextMap status] :: 312/528 (59.09%) texture blocks written to disk
[PretextMap status] :: 313/528 (59.28%) texture blocks written to disk
[PretextMap status] :: 314/528 (59.47%) texture blocks written to disk
[PretextMap status] :: 315/528 (59.66%) texture blocks written to disk
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[PretextMap status] :: 317/528 (60.04%) texture blocks written to disk
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[PretextMap status] :: 319/528 (60.42%) texture blocks written to disk
[PretextMap status] :: 320/528 (60.61%) texture blocks written to disk
[PretextMap status] :: 321/528 (60.80%) texture blocks written to disk
[PretextMap status] :: 322/528 (60.98%) texture blocks written to disk
[PretextMap status] :: 323/528 (61.17%) texture blocks written to disk
[PretextMap status] :: 324/528 (61.36%) texture blocks written to disk
[PretextMap status] :: 325/528 (61.55%) texture blocks written to disk
[PretextMap status] :: 326/528 (61.74%) texture blocks written to disk
[PretextMap status] :: 327/528 (61.93%) texture blocks written to disk
[PretextMap status] :: 328/528 (62.12%) texture blocks written to disk
[PretextMap status] :: 329/528 (62.31%) texture blocks written to disk
[PretextMap status] :: 330/528 (62.50%) texture blocks written to disk
[PretextMap status] :: 331/528 (62.69%) texture blocks written to disk
[PretextMap status] :: 332/528 (62.88%) texture blocks written to disk
[PretextMap status] :: 333/528 (63.07%) texture blocks written to disk
[PretextMap status] :: 334/528 (63.26%) texture blocks written to disk
[PretextMap status] :: 335/528 (63.45%) texture blocks written to disk
[PretextMap status] :: 336/528 (63.64%) texture blocks written to disk
[PretextMap status] :: 337/528 (63.83%) texture blocks written to disk
[PretextMap status] :: 338/528 (64.02%) texture blocks written to disk
[PretextMap status] :: 339/528 (64.20%) texture blocks written to disk
[PretextMap status] :: 340/528 (64.39%) texture blocks written to disk
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[PretextMap status] :: 344/528 (65.15%) texture blocks written to disk
[PretextMap status] :: 345/528 (65.34%) texture blocks written to disk
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[PretextMap status] :: 349/528 (66.10%) texture blocks written to disk
[PretextMap status] :: 350/528 (66.29%) texture blocks written to disk
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[PretextMap status] :: 352/528 (66.67%) texture blocks written to disk
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[PretextMap status] :: 355/528 (67.23%) texture blocks written to disk
[PretextMap status] :: 356/528 (67.42%) texture blocks written to disk
[PretextMap status] :: 357/528 (67.61%) texture blocks written to disk
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Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpvdvotu4c/files/f/b/8/dataset_fb89d026-ef8e-4ad9-8c41-d71f16980b3e.dat' input.fasta && ln -s '/tmp/tmpvdvotu4c/files/c/a/1/dataset_ca1ee6de-2d54-43a5-8c89-325e6011c8a7.dat' input.bam && samtools faidx input.fasta && mkdir initial_break agp_out agp_break final_outs && yahs --no-mem-check input.fasta input.bam -e 'GATC,GANTC,CTNAG,TTAA' --no-contig-ec  -o yahs_out 2> output.log && ls -lah && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/yahs/ff4031bfaa22/yahs/move_files.py' && ls -lah ./*

Exit Code:

```
0
```

Standard Output:

total 8M     
drwxr-xr-x    6 1001     127         4.0K Sep 23 14:52 .
drwxr-xr-x   12 1001     127         4.0K Sep 23 14:52 ..
drwxr-xr-x    2 1001     127         4.0K Sep 23 14:52 agp_break
drwxr-xr-x    2 1001     127         4.0K Sep 23 14:52 agp_out
drwxr-xr-x    2 1001     127         4.0K Sep 23 14:52 final_outs
drwxr-xr-x    2 1001     127         4.0K Sep 23 14:52 initial_break
lrwxrwxrwx    1 1001     127           77 Sep 23 14:52 input.bam -> /tmp/tmpvdvotu4c/files/c/a/1/dataset_ca1ee6de-2d54-43a5-8c89-325e6011c8a7.dat
lrwxrwxrwx    1 1001     127           77 Sep 23 14:52 input.fasta -> /tmp/tmpvdvotu4c/files/f/b/8/dataset_fb89d026-ef8e-4ad9-8c41-d71f16980b3e.dat
-rw-r--r--    1 1001     127         3.5K Sep 23 14:52 input.fasta.fai
-rw-r--r--    1 1001     127         5.1K Sep 23 14:52 output.log
-rw-r--r--    1 1001     127         5.6M Sep 23 14:52 yahs_out.bin
-rw-r--r--    1 1001     127         4.2K Sep 23 14:52 yahs_out_no_break.agp
-rw-r--r--    1 1001     127         4.2K Sep 23 14:52 yahs_out_scaffolds_final.agp
-rw-r--r--    1 1001     127         1.9M Sep 23 14:52 yahs_out_scaffolds_final.fa
lrwxrwxrwx    1 1001     127           77 Sep 23 14:52 ./input.bam -> /tmp/tmpvdvotu4c/files/c/a/1/dataset_ca1ee6de-2d54-43a5-8c89-325e6011c8a7.dat
lrwxrwxrwx    1 1001     127           77 Sep 23 14:52 ./input.fasta -> /tmp/tmpvdvotu4c/files/f/b/8/dataset_fb89d026-ef8e-4ad9-8c41-d71f16980b3e.dat
-rw-r--r--    1 1001     127         3.5K Sep 23 14:52 ./input.fasta.fai
-rw-r--r--    1 1001     127         5.1K Sep 23 14:52 ./output.log
-rw-r--r--    1 1001     127         5.6M Sep 23 14:52 ./yahs_out.bin

./agp_break:
total 16K    
drwxr-xr-x    2 1001     127         4.0K Sep 23 14:52 .
drwxr-xr-x    6 1001     127         4.0K Sep 23 14:52 ..
-rw-r--r--    1 1001     127         4.2K Sep 23 14:52 yahs_out_no_break.agp

./agp_out:
total 8K     
drwxr-xr-x    2 1001     127         4.0K Sep 23 14:52 .
drwxr-xr-x    6 1001     127         4.0K Sep 23 14:52 ..

./final_outs:
total 2M     
drwxr-xr-x    2 1001     127         4.0K Sep 23 14:52 .
drwxr-xr-x    6 1001     127         4.0K Sep 23 14:52 ..
-rw-r--r--    1 1001     127         4.2K Sep 23 14:52 yahs_out_scaffolds_final.agp
-rw-r--r--    1 1001     127         1.9M Sep 23 14:52 yahs_out_scaffolds_final.fa

./initial_break:
total 8K     
drwxr-xr-x    2 1001     127         4.0K Sep 23 14:52 .
drwxr-xr-x    6 1001     127         4.0K Sep 23 14:52 ..

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function	`{"__current_case__": 0, "agp": null, "bfile": {"values": [{"id": 10, "src": "hda"}]}, "enzyme_conditional": {"__current_case__": 1, "enzyme_options": "preconfigured", "preconfigured_enzymes": "arima2"}, "fasta": {"values": [{"id": 7, "src": "hda"}]}, "function_select": "yahs", "length": null, "no_contig_ec": true, "no_scaffold_ec": false, "quality": null, "res": ""}`
log_out	`true`

Step 19: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmpvdvotu4c/files/7/6/e/dataset_76e28374-b431-43e4-8a14-da877215f179.dat -f png -r 1000 -c 5 --sequences '=full' --minTexels 64 --gridSize 0 '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmpvdvotu4c/files/7/6/e/dataset_76e28374-b431-43e4-8a14-da877215f179.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 1000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 0 pixels
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 1, "showGrid": "no"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmpvdvotu4c/job_working_directory/000/14/outputs/dataset_bce6eeca-8347-4237-ab1e-f14db42ac13b.dat' -g  -w  -r 'scaffold_[0-9]*' '$&.hap1' '/tmp/tmpvdvotu4c/files/c/a/1/dataset_ca196f4c-5185-4c0d-9dca-85c5ea8b3f39.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "scaffold_[0-9]*", "global": true, "is_regex": true, "replace_pattern": "$&.hap1", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": true}]`

Step 3: Sequence graph:
- step_state: scheduled

Step 21: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpvdvotu4c/files/f/b/8/dataset_fb89d026-ef8e-4ad9-8c41-d71f16980b3e.dat' --agp-to-path /tmp/tmpvdvotu4c/files/b/c/e/dataset_bce6eeca-8347-4237-ab1e-f14db42ac13b.dat  -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 84
Total scaffold length: 1982895
Average scaffold length: 23605.89
Scaffold N50: 20934
Scaffold auN: 33899.67
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 84
Total contig length: 1982895
Average contig length: 23605.89
Contig N50: 20934
Contig auN: 33899.67
Contig L50: 30
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 606458:383991:386001:606445
GC content %: 38.83
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 84

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 2, "agp_to_path": {"values": [{"id": 15, "src": "hda"}]}, "discover_paths": false, "selector": "scaffolding"}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpvdvotu4c/files/c/f/b/dataset_cfbd1ab4-1f08-43b1-bffa-124891034231.dat'  -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 84
Total scaffold length: 1982895
Average scaffold length: 23605.89
Scaffold N50: 20934
Scaffold auN: 33899.67
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 84
Total contig length: 1982895
Average contig length: 23605.89
Contig N50: 20934
Contig auN: 33899.67
Contig L50: 30
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 606458:383991:386001:606445
GC content %: 38.83
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 84

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpvdvotu4c/files/c/f/b/dataset_cfbd1ab4-1f08-43b1-bffa-124891034231.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmpvdvotu4c/job_working_directory/000/17/outputs/dataset_da5a3150-2d69-44a2-8d92-7c82cef530f6.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpvdvotu4c/files/c/f/b/dataset_cfbd1ab4-1f08-43b1-bffa-124891034231.dat' --out-size s   --tabular > '/tmp/tmpvdvotu4c/job_working_directory/000/18/outputs/dataset_df7c7eba-7e03-4ebd-8325-10b8db6b3339.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "s", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpvdvotu4c/files/a/6/3/dataset_a63ef9da-881c-4a56-a9b9-cad62a47b5e1.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpvdvotu4c/files/2/3/c/dataset_23cc1cd1-97f3-451a-8a76-4044b392dcb9.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpvdvotu4c/job_working_directory/000/19/outputs/dataset_9ff8dcae-a1e5-4513-90b4-16591a835b2a.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 136120731
ref seq len = 3965790
binary seq ticks = 69001016
build suffix-array ticks = 736742073
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 195820366
Total time taken: 0.4762
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 1307277
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000037, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000037 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000053, nseq: 100108
	[0000][ M::kt_pipeline] read 100108 sequences (10000053 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 7.163 CPU sec, 9.124 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000072, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000072 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100108 reads in 6.971 CPU sec, 8.818 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000203, nseq: 100132
	[0000][ M::kt_pipeline] read 100132 sequences (10000203 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 7.087 CPU sec, 8.914 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000073, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000073 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100132 reads in 6.969 CPU sec, 9.154 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000141, nseq: 100166
	[0000][ M::kt_pipeline] read 100166 sequences (10000141 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 6.843 CPU sec, 8.687 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000104, nseq: 118598
	[0000][ M::kt_pipeline] read 118598 sequences (10000104 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100166 reads in 6.896 CPU sec, 8.278 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000109, nseq: 151884
	[0000][ M::kt_pipeline] read 151884 sequences (10000109 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118598 reads in 6.656 CPU sec, 8.238 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000126, nseq: 151908
	[0000][ M::kt_pipeline] read 151908 sequences (10000126 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151884 reads in 6.230 CPU sec, 7.163 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151908 reads in 6.104 CPU sec, 7.300 real sec
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000007, nseq: 151868
	[0000][ M::kt_pipeline] read 151868 sequences (10000007 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 6.285 CPU sec, 7.506 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000077, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000077 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151868 reads in 6.388 CPU sec, 7.804 real sec
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000024, nseq: 127818
	[0000][ M::kt_pipeline] read 127818 sequences (10000024 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 5.864 CPU sec, 7.752 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000071, nseq: 98956
	[0000][ M::kt_pipeline] read 98956 sequences (10000071 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127818 reads in 8.023 CPU sec, 10.097 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000004, nseq: 145156
	[0000][ M::kt_pipeline] read 145156 sequences (10000004 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98956 reads in 10.563 CPU sec, 13.581 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3496096, nseq: 53016
	[0000][ M::kt_pipeline] read 53016 sequences (3496096 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145156 reads in 9.082 CPU sec, 11.227 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 53016 reads in 3.162 CPU sec, 3.799 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2446.760414 MHz
Runtime profile:

	Time taken for main_mem function: 137.71 sec

	IO times (sec) :
	Reading IO time (reads) avg: 6.56, (6.56, 6.56)
	Writing IO time (SAM) avg: 6.00, (6.00, 6.00)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 137.70
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 137.37, (137.37, 137.37)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 12.65, (12.65, 12.65)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 124.72, (124.72, 124.72)
		SMEM compute avg: 40.22, (40.22, 40.22)
		SAL compute avg: 24.46, (24.46, 24.46)
				MEM_SA avg: 12.42, (12.42, 12.42)

		BSW time, avg: 52.36, (52.36, 52.36)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[1307277] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 2, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 17, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpvdvotu4c/files/a/6/3/dataset_a63ef9da-881c-4a56-a9b9-cad62a47b5e1.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpvdvotu4c/files/8/9/a/dataset_89a3de3f-59a2-44b7-bde0-edb0b2676323.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpvdvotu4c/job_working_directory/000/20/outputs/dataset_870fd62e-fe88-4290-84e9-dec3ceb24014.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 134880622
ref seq len = 3965790
binary seq ticks = 105589580
build suffix-array ticks = 744362675
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 197642558
Total time taken: 0.5008
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 1307277
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000036, nseq: 100212
	[0000][ M::kt_pipeline] read 100212 sequences (10000036 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000140, nseq: 100074
	[0000][ M::kt_pipeline] read 100074 sequences (10000140 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100212 reads in 7.173 CPU sec, 9.037 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000066, nseq: 100106
	[0000][ M::kt_pipeline] read 100106 sequences (10000066 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100074 reads in 7.003 CPU sec, 9.252 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000070, nseq: 100180
	[0000][ M::kt_pipeline] read 100180 sequences (10000070 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100106 reads in 7.260 CPU sec, 9.693 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000000, nseq: 100202
	[0000][ M::kt_pipeline] read 100202 sequences (10000000 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100180 reads in 6.965 CPU sec, 8.960 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000132, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000132 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100202 reads in 6.859 CPU sec, 8.303 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 118588
	[0000][ M::kt_pipeline] read 118588 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 6.814 CPU sec, 8.530 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000125, nseq: 151900
	[0000][ M::kt_pipeline] read 151900 sequences (10000125 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118588 reads in 6.682 CPU sec, 8.421 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000005, nseq: 151874
	[0000][ M::kt_pipeline] read 151874 sequences (10000005 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151900 reads in 6.201 CPU sec, 7.333 real sec
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151904
	[0000][ M::kt_pipeline] read 151904 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151874 reads in 6.103 CPU sec, 6.997 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151896
	[0000][ M::kt_pipeline] read 151896 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151904 reads in 6.027 CPU sec, 7.050 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000130, nseq: 151906
	[0000][ M::kt_pipeline] read 151906 sequences (10000130 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151896 reads in 6.114 CPU sec, 7.039 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 127808
	[0000][ M::kt_pipeline] read 127808 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151906 reads in 5.817 CPU sec, 7.487 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000028, nseq: 98948
	[0000][ M::kt_pipeline] read 98948 sequences (10000028 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127808 reads in 8.013 CPU sec, 10.157 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000026, nseq: 145218
	[0000][ M::kt_pipeline] read 145218 sequences (10000026 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98948 reads in 10.757 CPU sec, 13.737 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3489223, nseq: 52906
	[0000][ M::kt_pipeline] read 52906 sequences (3489223 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145218 reads in 9.060 CPU sec, 10.880 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 52906 reads in 3.109 CPU sec, 3.744 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.619547 MHz
Runtime profile:

	Time taken for main_mem function: 137.12 sec

	IO times (sec) :
	Reading IO time (reads) avg: 6.43, (6.43, 6.43)
	Writing IO time (SAM) avg: 5.41, (5.41, 5.41)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 137.10
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 136.61, (136.61, 136.61)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 13.32, (13.32, 13.32)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 123.28, (123.28, 123.28)
		SMEM compute avg: 38.87, (38.87, 38.87)
		SAL compute avg: 23.50, (23.50, 23.50)
				MEM_SA avg: 11.90, (11.90, 11.90)

		BSW time, avg: 53.63, (53.63, 53.63)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[1307277] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 3, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 17, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

busco --in '/tmp/tmpvdvotu4c/files/a/6/3/dataset_a63ef9da-881c-4a56-a9b9-cad62a47b5e1.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'vertebrata_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific

Exit Code:

```
1
```

Standard Error:

2024-09-23 15:12:39 ERROR:	Something went wrong. Results not recorded.
2024-09-23 15:12:39 ERROR:	BUSCO analysis failed!
2024-09-23 15:12:39 ERROR:	Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

Standard Output:

2024-09-23 14:54:04 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 09/23/2024 14:54:04 *****
2024-09-23 14:54:04 INFO:	Configuring BUSCO with local environment
2024-09-23 14:54:04 INFO:	Running genome mode
2024-09-23 14:54:06 INFO:	Input file is /tmp/tmpvdvotu4c/files/a/6/3/dataset_a63ef9da-881c-4a56-a9b9-cad62a47b5e1.dat
2024-09-23 14:54:06 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-09-23 14:54:06 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-09-23 14:54:06 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2024-09-23 14:54:06 INFO:	Running 1 job(s) on bbtools, starting at 09/23/2024 14:54:06
2024-09-23 14:54:08 INFO:	[bbtools]	1 of 1 task(s) completed
2024-09-23 14:54:08 INFO:	Running 1 job(s) on miniprot_index, starting at 09/23/2024 14:54:08
2024-09-23 14:54:09 INFO:	[miniprot_index]	1 of 1 task(s) completed
2024-09-23 14:54:09 INFO:	Running 1 job(s) on miniprot_align, starting at 09/23/2024 14:54:09
2024-09-23 15:11:37 INFO:	[miniprot_align]	1 of 1 task(s) completed
2024-09-23 15:11:44 INFO:	***** Run HMMER on gene sequences *****
2024-09-23 15:11:45 INFO:	Running 607 job(s) on hmmsearch, starting at 09/23/2024 15:11:45
2024-09-23 15:11:52 INFO:	[hmmsearch]	61 of 607 task(s) completed
2024-09-23 15:11:57 INFO:	[hmmsearch]	122 of 607 task(s) completed
2024-09-23 15:12:03 INFO:	[hmmsearch]	183 of 607 task(s) completed
2024-09-23 15:12:08 INFO:	[hmmsearch]	243 of 607 task(s) completed
2024-09-23 15:12:13 INFO:	[hmmsearch]	304 of 607 task(s) completed
2024-09-23 15:12:18 INFO:	[hmmsearch]	365 of 607 task(s) completed
2024-09-23 15:12:23 INFO:	[hmmsearch]	425 of 607 task(s) completed
2024-09-23 15:12:28 INFO:	[hmmsearch]	486 of 607 task(s) completed
2024-09-23 15:12:33 INFO:	[hmmsearch]	547 of 607 task(s) completed
2024-09-23 15:12:38 INFO:	[hmmsearch]	607 of 607 task(s) completed
2024-09-23 15:12:38 INFO:	46 exons in total
2024-09-23 15:12:38 WARNING:	2 of 36 Complete matches (5.6%) contain internal stop codons in Miniprot gene predictions
2024-09-23 15:12:38 WARNING:	BUSCO gene predictions from Miniprot have low average identity (0.4699999988079071). You may want to repeat the analysis using the Metaeuk pipeline.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image"]`

Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmpvdvotu4c/job_working_directory/000/22/outputs/dataset_52cd1fb2-3923-4775-979d-10672767c29a.dat' -g     '#' 'Number of' '/tmp/tmpvdvotu4c/files/d/a/5/dataset_da5a3150-2d69-44a2-8d92-7c82cef530f6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 30: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpvdvotu4c/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmpvdvotu4c/files/d/f/7/dataset_df7c7eba-7e03-4ebd-8325-10b8db6b3339.dat' --output='/tmp/tmpvdvotu4c/job_working_directory/000/23/outputs/dataset_00a236e8-943a-4b09-9109-f737c9b59156.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e4b0412379ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpvdvotu4c/job_working_directory/000/24/configs/tmpi96o1u_u' '/tmp/tmpvdvotu4c/files/0/0/a/dataset_00a236e8-943a-4b09-9109-f737c9b59156.dat' > '/tmp/tmpvdvotu4c/job_working_directory/000/24/outputs/dataset_91fcdcfd-1c88-4c08-b72f-ebc77f4aa07e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412379ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmpvdvotu4c/files/9/1/f/dataset_91fcdcfd-1c88-4c08-b72f-ebc77f4aa07e.dat > '/tmp/tmpvdvotu4c/job_working_directory/000/25/outputs/dataset_ac0793fd-19e6-4473-9efd-8eaed51c6c37.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412379ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpvdvotu4c/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpvdvotu4c/files/9/1/f/dataset_91fcdcfd-1c88-4c08-b72f-ebc77f4aa07e.dat' '/tmp/tmpvdvotu4c/job_working_directory/000/26/outputs/dataset_48916a89-871f-42e3-a35c-277aa8c04e95.dat' '1' yes

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412379ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e4b0412379ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412379ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1982895", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmpvdvotu4c/job_working_directory/000/35/configs/tmpq15pbg0b' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpvdvotu4c/files/4/8/9/dataset_48916a89-871f-42e3-a35c-277aa8c04e95.dat' '/tmp/tmpvdvotu4c/job_working_directory/000/35/outputs/dataset_5dc85f41-0c3b-4286-95e4-ee220000618e.dat'

Exit Code:

```
0
```

Standard Output:

c3/1982895
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1982895;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 84 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412379ba11efad02cfb41fee9136"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1982895"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 4: Database for Busco Lineage:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpvdvotu4c/files/9/f/f/dataset_9ff8dcae-a1e5-4513-90b4-16591a835b2a.dat' 'forward_input.bam' && ln -s '/tmp/tmpvdvotu4c/files/8/7/0/dataset_870fd62e-fe88-4290-84e9-dec3ceb24014.dat' 'reverse_input.bam' && bellerophon --forward forward_input.bam --reverse reverse_input.bam --quality 20 --output 'merged_out.bam' --threads ${GALAXY_SLOTS:-1} && samtools sort --no-PG -O BAM -o '/tmp/tmpvdvotu4c/job_working_directory/000/28/outputs/dataset_dbfea95e-3d42-4d18-8889-a98388a7c4a5.dat' -@ ${GALAXY_SLOTS:-1} merged_out.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 32: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpvdvotu4c/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpvdvotu4c/files/5/d/c/dataset_5dc85f41-0c3b-4286-95e4-ee220000618e.dat' 'c5,c6' T '/tmp/tmpvdvotu4c/job_working_directory/000/36/outputs/dataset_eb8fa333-63a6-49a4-b2be-a68d924ed210.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 33: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpvdvotu4c/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpvdvotu4c/files/5/d/c/dataset_5dc85f41-0c3b-4286-95e4-ee220000618e.dat' 'c4,c7' T '/tmp/tmpvdvotu4c/job_working_directory/000/37/outputs/dataset_8a93ab51-c766-4dc1-806f-b5ec3fe6c428.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 34: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmpvdvotu4c/files/d/b/f/dataset_dbfea95e-3d42-4d18-8889-a98388a7c4a5.dat' | PretextMap -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 84 sequences, sorted by length, descending. Filtering by minimum mapping quality 10

                                                                                
[PretextMap status] :: 10.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 10.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 15.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 20.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 25.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 30.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 35.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 40.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 45.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 50.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 55.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 60.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 65.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 70.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 75.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 80.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 85.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 90.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 95.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 100.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 105.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 109.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 115.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 120.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 125.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 130.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 135.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 139.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 144.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 150.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 155.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 159.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 165.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 169.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 174.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 179.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 185.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 190.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 195.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 200.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 204.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 210.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 215.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 220.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 224.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 229.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 234.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 239.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 244.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 250.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 255.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 260.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 265.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 270.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 275.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 280.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 285.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 290.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 295.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 300.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 305.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 310.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 315.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 640.0 k reads processed, 320.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 650.0 k reads processed, 325.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 660.0 k reads processed, 330.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 670.0 k reads processed, 335.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 680.0 k reads processed, 340.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 690.0 k reads processed, 345.0 k read-pairs mapped
[PretextMap status] :: Creating MipMaps...
[PretextMap status] :: Equalising contrast...
[PretextMap status] :: Compressing textures...

[PretextMap status] ::   1/528 (0.19%) texture blocks written to disk
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[PretextMap status] :: 522/528 (98.86%) texture blocks written to disk
[PretextMap status] :: 523/528 (99.05%) texture blocks written to disk
[PretextMap status] :: 524/528 (99.24%) texture blocks written to disk
[PretextMap status] :: 525/528 (99.43%) texture blocks written to disk
[PretextMap status] :: 526/528 (99.62%) texture blocks written to disk
[PretextMap status] :: 527/528 (99.81%) texture blocks written to disk
[PretextMap status] :: 528/528 (100.00%) texture blocks written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpvdvotu4c/files/d/b/f/dataset_dbfea95e-3d42-4d18-8889-a98388a7c4a5.dat' ./input.bam &&  bedtools bamtobed -bed12   -i ./input.bam > '/tmp/tmpvdvotu4c/job_working_directory/000/30/outputs/dataset_46630510-e475-4d06-bc5a-122e70ce6086.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ed_score	`false`
option	`"-bed12"`
split	`false`
tag	`""`

Step 36: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpvdvotu4c/job_working_directory/000/38/configs/tmpwyd5mbee' && Rscript '/tmp/tmpvdvotu4c/job_working_directory/000/38/configs/tmpwyd5mbee'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpvdvotu4c/files/e/b/8/dataset_eb8fa333-63a6-49a4-b2be-a68d924ed210.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpvdvotu4c/job_working_directory/000/38/outputs/dataset_693d4b90-63a1-4f70-96bd-634130f88639.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"x"`
xplot	`"1"`
ylab	`"Nx (Mb)"`
yplot	`"2"`

Step 37: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpvdvotu4c/job_working_directory/000/39/configs/tmpv2uogvli' && Rscript '/tmp/tmpvdvotu4c/job_working_directory/000/39/configs/tmpv2uogvli'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpvdvotu4c/files/8/a/9/dataset_8a93ab51-c766-4dc1-806f-b5ec3fe6c428.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpvdvotu4c/job_working_directory/000/39/outputs/dataset_33d5dd3c-caba-454b-a9d0-7474e59fd2c5.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"1"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"2"`

Step 38: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmpvdvotu4c/files/a/9/0/dataset_a906ed56-3831-4ce7-813b-3543e50a3ed3.dat -f png -r 1000 -c 5 --sequences '=full' --minTexels 64 --gridSize 1 --gridColour black '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmpvdvotu4c/files/a/9/0/dataset_a906ed56-3831-4ce7-813b-3543e50a3ed3.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 1000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 1 pixel
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 0, "gridcolor": "black", "gridsize": "1", "showGrid": "yes"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 39: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

( LC_ALL=C  sort   --stable -t '	'  -k '4,4'  ) < '/tmp/tmpvdvotu4c/files/4/6/6/dataset_46630510-e475-4d06-bc5a-122e70ce6086.dat' > '/tmp/tmpvdvotu4c/job_working_directory/000/32/outputs/dataset_be362112-2205-4fe0-9c68-71fa6a7cf116.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
chromInfo	`"/tmp/tmpvdvotu4c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`"0"`
ignore_case	`false`
sortkeys	`[{"__index__": 0, "column": "4", "order": "", "style": ""}]`
unique	`false`

Step 40: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"e4b0412279ba11efad02cfb41fee9136"`
input	`{"values": [{"id": 5, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 5: Lineage:
- step_state: scheduled
Step 6: HiC Forward reads:
- step_state: scheduled
Step 7: HiC reverse reads:
- step_state: scheduled
Step 8: Restriction enzymes:
- step_state: scheduled
Step 9: Estimated genome size - Parameter File:
- step_state: scheduled
Step 10: SAK input file:
- step_state: scheduled

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 143b5dbe56ed6ef9
- history_state
  - error
- invocation_id
  - 143b5dbe56ed6ef9
- invocation_state
  - scheduled
- workflow_id
  - b82b96c8ab86261b

gxydevbot · 2024-09-24T13:41:54Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-24T14:13:45Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input GFA:
- step_state: scheduled
Step 2: Haplotype:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "$&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "hap1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 12: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp7mwsax3_/files/6/1/e/dataset_61e19c18-3e8f-440d-8d42-fe72e90f34d0.dat'  -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 84
Total scaffold length: 1982895
Average scaffold length: 23605.89
Scaffold N50: 20934
Scaffold auN: 33899.67
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 84
Total contig length: 1982895
Average contig length: 23605.89
Contig N50: 20934
Contig auN: 33899.67
Contig L50: 30
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 606458:383991:386001:606445
GC content %: 38.83
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 84
# edges: 4
Average degree: 0.05
# connected components: 1
Largest connected component length: 94650
# dead ends: 165
# disconnected components: 81
Total length disconnected components: 1888245
# separated components: 82
# bubbles: 0
# circular segments: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp7mwsax3_/files/7/8/d/dataset_78dbdb30-4a36-4f0b-98e3-a08a6655de4a.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmp7mwsax3_/files/d/3/e/dataset_d3e2e9d9-3014-4a2f-bcd0-865cde644387.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp7mwsax3_/job_working_directory/000/8/outputs/dataset_2ce5c565-639e-483a-9db8-9ff40898727a.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 130700616
ref seq len = 3965790
binary seq ticks = 70241965
build suffix-array ticks = 648696246
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 176142456
Total time taken: 0.4301
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 3041008
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000037, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000037 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000053, nseq: 100108
	[0000][ M::kt_pipeline] read 100108 sequences (10000053 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 5.165 CPU sec, 5.168 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000072, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000072 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100108 reads in 5.259 CPU sec, 5.330 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000203, nseq: 100132
	[0000][ M::kt_pipeline] read 100132 sequences (10000203 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 5.239 CPU sec, 5.320 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000073, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000073 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100132 reads in 5.168 CPU sec, 5.235 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000141, nseq: 100166
	[0000][ M::kt_pipeline] read 100166 sequences (10000141 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 5.125 CPU sec, 5.206 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000104, nseq: 118598
	[0000][ M::kt_pipeline] read 118598 sequences (10000104 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100166 reads in 5.266 CPU sec, 5.346 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000109, nseq: 151884
	[0000][ M::kt_pipeline] read 151884 sequences (10000109 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118598 reads in 5.078 CPU sec, 5.157 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000126, nseq: 151908
	[0000][ M::kt_pipeline] read 151908 sequences (10000126 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151884 reads in 4.751 CPU sec, 4.835 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151908 reads in 4.876 CPU sec, 4.982 real sec
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000007, nseq: 151868
	[0000][ M::kt_pipeline] read 151868 sequences (10000007 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 5.020 CPU sec, 5.125 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000077, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000077 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151868 reads in 4.933 CPU sec, 5.015 real sec
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000024, nseq: 127818
	[0000][ M::kt_pipeline] read 127818 sequences (10000024 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 4.918 CPU sec, 5.022 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000071, nseq: 98956
	[0000][ M::kt_pipeline] read 98956 sequences (10000071 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127818 reads in 6.353 CPU sec, 6.451 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000004, nseq: 145156
	[0000][ M::kt_pipeline] read 145156 sequences (10000004 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98956 reads in 8.277 CPU sec, 8.374 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3496096, nseq: 53016
	[0000][ M::kt_pipeline] read 53016 sequences (3496096 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145156 reads in 7.231 CPU sec, 7.312 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 53016 reads in 2.606 CPU sec, 2.697 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.588804 MHz
Runtime profile:

	Time taken for main_mem function: 86.83 sec

	IO times (sec) :
	Reading IO time (reads) avg: 5.05, (5.05, 5.05)
	Writing IO time (SAM) avg: 3.60, (3.60, 3.60)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 86.82
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 86.57, (86.57, 86.57)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 7.98, (7.98, 7.98)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 78.58, (78.58, 78.58)
		SMEM compute avg: 25.21, (25.21, 25.21)
		SAL compute avg: 16.51, (16.51, 16.51)
				MEM_SA avg: 8.12, (8.12, 8.12)

		BSW time, avg: 31.96, (31.96, 31.96)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[3041008] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 2, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 7, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp7mwsax3_/files/7/8/d/dataset_78dbdb30-4a36-4f0b-98e3-a08a6655de4a.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmp7mwsax3_/files/3/0/9/dataset_309d290e-dc69-4f0e-a822-947568df4cc5.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp7mwsax3_/job_working_directory/000/9/outputs/dataset_8b333305-5ec5-48f2-ab36-1df740333a65.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 121082650
ref seq len = 3965790
binary seq ticks = 72443756
build suffix-array ticks = 603091265
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 175385161
Total time taken: 0.4108
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 3041008
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000036, nseq: 100212
	[0000][ M::kt_pipeline] read 100212 sequences (10000036 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000140, nseq: 100074
	[0000][ M::kt_pipeline] read 100074 sequences (10000140 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100212 reads in 5.111 CPU sec, 5.120 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000066, nseq: 100106
	[0000][ M::kt_pipeline] read 100106 sequences (10000066 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100074 reads in 5.123 CPU sec, 5.197 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000070, nseq: 100180
	[0000][ M::kt_pipeline] read 100180 sequences (10000070 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100106 reads in 5.265 CPU sec, 5.352 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000000, nseq: 100202
	[0000][ M::kt_pipeline] read 100202 sequences (10000000 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100180 reads in 5.020 CPU sec, 5.100 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000132, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000132 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100202 reads in 5.116 CPU sec, 5.205 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 118588
	[0000][ M::kt_pipeline] read 118588 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 5.218 CPU sec, 5.297 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000125, nseq: 151900
	[0000][ M::kt_pipeline] read 151900 sequences (10000125 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118588 reads in 5.065 CPU sec, 5.155 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000005, nseq: 151874
	[0000][ M::kt_pipeline] read 151874 sequences (10000005 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151900 reads in 4.748 CPU sec, 4.832 real sec
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151904
	[0000][ M::kt_pipeline] read 151904 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151874 reads in 4.726 CPU sec, 4.831 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151896
	[0000][ M::kt_pipeline] read 151896 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151904 reads in 5.014 CPU sec, 5.122 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000130, nseq: 151906
	[0000][ M::kt_pipeline] read 151906 sequences (10000130 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151896 reads in 4.756 CPU sec, 4.860 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 127808
	[0000][ M::kt_pipeline] read 127808 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151906 reads in 4.866 CPU sec, 4.974 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000028, nseq: 98948
	[0000][ M::kt_pipeline] read 98948 sequences (10000028 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127808 reads in 6.423 CPU sec, 6.521 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000026, nseq: 145218
	[0000][ M::kt_pipeline] read 145218 sequences (10000026 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98948 reads in 8.290 CPU sec, 8.374 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3489223, nseq: 52906
	[0000][ M::kt_pipeline] read 52906 sequences (3489223 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145218 reads in 7.133 CPU sec, 7.218 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 52906 reads in 2.601 CPU sec, 2.704 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.507092 MHz
Runtime profile:

	Time taken for main_mem function: 86.10 sec

	IO times (sec) :
	Reading IO time (reads) avg: 4.97, (4.97, 4.97)
	Writing IO time (SAM) avg: 3.83, (3.83, 3.83)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 86.09
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 85.86, (85.86, 85.86)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 7.73, (7.73, 7.73)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 78.13, (78.13, 78.13)
		SMEM compute avg: 25.23, (25.23, 25.23)
		SAL compute avg: 16.66, (16.66, 16.66)
				MEM_SA avg: 8.23, (8.23, 8.23)

		BSW time, avg: 31.56, (31.56, 31.56)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[3041008] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 3, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 7, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp7mwsax3_/files/2/c/e/dataset_2ce5c565-639e-483a-9db8-9ff40898727a.dat' 'forward_input.bam' && ln -s '/tmp/tmp7mwsax3_/files/8/b/3/dataset_8b333305-5ec5-48f2-ab36-1df740333a65.dat' 'reverse_input.bam' && bellerophon --forward forward_input.bam --reverse reverse_input.bam --quality 20 --output 'merged_out.bam' --threads ${GALAXY_SLOTS:-1} && samtools sort --no-PG -O BAM -o '/tmp/tmp7mwsax3_/job_working_directory/000/10/outputs/dataset_a00d6328-f179-4f3e-87da-6fbecb456263.dat' -@ ${GALAXY_SLOTS:-1} merged_out.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmp7mwsax3_/files/a/0/0/dataset_a00d6328-f179-4f3e-87da-6fbecb456263.dat' | PretextMap -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 84 sequences, sorted by length, descending. Filtering by minimum mapping quality 10

                                                                                
[PretextMap status] :: 10.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 10.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 15.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 20.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 25.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 30.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 35.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 40.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 45.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 50.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 55.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 60.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 65.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 70.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 75.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 80.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 85.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 90.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 95.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 100.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 104.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 109.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 114.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 119.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 124.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 129.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 134.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 139.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 145.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 150.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 154.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 159.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 165.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 170.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 175.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 180.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 185.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 190.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 195.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 200.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 205.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 210.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 215.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 220.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 225.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 230.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 235.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 240.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 245.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 250.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 255.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 260.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 265.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 270.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 275.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 280.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 285.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 290.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 295.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 300.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 305.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 310.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 315.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 640.0 k reads processed, 320.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 650.0 k reads processed, 325.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 660.0 k reads processed, 330.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 670.0 k reads processed, 335.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 680.0 k reads processed, 340.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 690.0 k reads processed, 345.0 k read-pairs mapped
[PretextMap status] :: Creating MipMaps...
[PretextMap status] :: Equalising contrast...
[PretextMap status] :: Compressing textures...

[PretextMap status] ::   1/528 (0.19%) texture blocks written to disk
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[PretextMap status] :: 526/528 (99.62%) texture blocks written to disk
[PretextMap status] :: 527/528 (99.81%) texture blocks written to disk
[PretextMap status] :: 528/528 (100.00%) texture blocks written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp7mwsax3_/files/7/8/d/dataset_78dbdb30-4a36-4f0b-98e3-a08a6655de4a.dat' input.fasta && ln -s '/tmp/tmp7mwsax3_/files/a/0/0/dataset_a00d6328-f179-4f3e-87da-6fbecb456263.dat' input.bam && samtools faidx input.fasta && mkdir initial_break agp_out agp_break final_outs && yahs --no-mem-check input.fasta input.bam -e 'GATC,GANTC,CTNAG,TTAA' --no-contig-ec  -o yahs_out 2> output.log && ls -lah && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/yahs/ff4031bfaa22/yahs/move_files.py' && ls -lah ./*

Exit Code:

```
0
```

Standard Output:

total 8M     
drwxr-xr-x    6 1001     127         4.0K Sep 24 13:52 .
drwxr-xr-x   12 1001     127         4.0K Sep 24 13:52 ..
drwxr-xr-x    2 1001     127         4.0K Sep 24 13:52 agp_break
drwxr-xr-x    2 1001     127         4.0K Sep 24 13:52 agp_out
drwxr-xr-x    2 1001     127         4.0K Sep 24 13:52 final_outs
drwxr-xr-x    2 1001     127         4.0K Sep 24 13:52 initial_break
lrwxrwxrwx    1 1001     127           77 Sep 24 13:52 input.bam -> /tmp/tmp7mwsax3_/files/a/0/0/dataset_a00d6328-f179-4f3e-87da-6fbecb456263.dat
lrwxrwxrwx    1 1001     127           77 Sep 24 13:52 input.fasta -> /tmp/tmp7mwsax3_/files/7/8/d/dataset_78dbdb30-4a36-4f0b-98e3-a08a6655de4a.dat
-rw-r--r--    1 1001     127         3.5K Sep 24 13:52 input.fasta.fai
-rw-r--r--    1 1001     127         5.1K Sep 24 13:52 output.log
-rw-r--r--    1 1001     127         5.6M Sep 24 13:52 yahs_out.bin
-rw-r--r--    1 1001     127         4.2K Sep 24 13:52 yahs_out_no_break.agp
-rw-r--r--    1 1001     127         4.2K Sep 24 13:52 yahs_out_scaffolds_final.agp
-rw-r--r--    1 1001     127         1.9M Sep 24 13:52 yahs_out_scaffolds_final.fa
lrwxrwxrwx    1 1001     127           77 Sep 24 13:52 ./input.bam -> /tmp/tmp7mwsax3_/files/a/0/0/dataset_a00d6328-f179-4f3e-87da-6fbecb456263.dat
lrwxrwxrwx    1 1001     127           77 Sep 24 13:52 ./input.fasta -> /tmp/tmp7mwsax3_/files/7/8/d/dataset_78dbdb30-4a36-4f0b-98e3-a08a6655de4a.dat
-rw-r--r--    1 1001     127         3.5K Sep 24 13:52 ./input.fasta.fai
-rw-r--r--    1 1001     127         5.1K Sep 24 13:52 ./output.log
-rw-r--r--    1 1001     127         5.6M Sep 24 13:52 ./yahs_out.bin

./agp_break:
total 16K    
drwxr-xr-x    2 1001     127         4.0K Sep 24 13:52 .
drwxr-xr-x    6 1001     127         4.0K Sep 24 13:52 ..
-rw-r--r--    1 1001     127         4.2K Sep 24 13:52 yahs_out_no_break.agp

./agp_out:
total 8K     
drwxr-xr-x    2 1001     127         4.0K Sep 24 13:52 .
drwxr-xr-x    6 1001     127         4.0K Sep 24 13:52 ..

./final_outs:
total 2M     
drwxr-xr-x    2 1001     127         4.0K Sep 24 13:52 .
drwxr-xr-x    6 1001     127         4.0K Sep 24 13:52 ..
-rw-r--r--    1 1001     127         4.2K Sep 24 13:52 yahs_out_scaffolds_final.agp
-rw-r--r--    1 1001     127         1.9M Sep 24 13:52 yahs_out_scaffolds_final.fa

./initial_break:
total 8K     
drwxr-xr-x    2 1001     127         4.0K Sep 24 13:52 .
drwxr-xr-x    6 1001     127         4.0K Sep 24 13:52 ..

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function	`{"__current_case__": 0, "agp": null, "bfile": {"values": [{"id": 10, "src": "hda"}]}, "enzyme_conditional": {"__current_case__": 1, "enzyme_options": "preconfigured", "preconfigured_enzymes": "arima2"}, "fasta": {"values": [{"id": 7, "src": "hda"}]}, "function_select": "yahs", "length": null, "no_contig_ec": true, "no_scaffold_ec": false, "quality": null, "res": ""}`
log_out	`true`

Step 19: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmp7mwsax3_/files/a/0/9/dataset_a09db4f0-d5d5-4380-9579-47e984f4ec5f.dat -f png -r 1000 -c 5 --sequences '=full' --minTexels 64 --gridSize 0 '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmp7mwsax3_/files/a/0/9/dataset_a09db4f0-d5d5-4380-9579-47e984f4ec5f.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 1000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 0 pixels
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 1, "showGrid": "no"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmp7mwsax3_/job_working_directory/000/14/outputs/dataset_89f411dc-921f-45a0-b050-6946d6017f5e.dat' -g  -w  -r 'scaffold_[0-9]*' '$&.hap1' '/tmp/tmp7mwsax3_/files/1/c/4/dataset_1c421a8a-0c35-4fa8-8b93-d8058fc9167d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "scaffold_[0-9]*", "global": true, "is_regex": true, "replace_pattern": "$&.hap1", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": true}]`

Step 3: Sequence graph:
- step_state: scheduled

Step 21: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp7mwsax3_/files/7/8/d/dataset_78dbdb30-4a36-4f0b-98e3-a08a6655de4a.dat' --agp-to-path /tmp/tmp7mwsax3_/files/8/9/f/dataset_89f411dc-921f-45a0-b050-6946d6017f5e.dat  -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 84
Total scaffold length: 1982895
Average scaffold length: 23605.89
Scaffold N50: 20934
Scaffold auN: 33899.67
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 84
Total contig length: 1982895
Average contig length: 23605.89
Contig N50: 20934
Contig auN: 33899.67
Contig L50: 30
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 606458:383991:386001:606445
GC content %: 38.83
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 84

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 2, "agp_to_path": {"values": [{"id": 15, "src": "hda"}]}, "discover_paths": false, "selector": "scaffolding"}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp7mwsax3_/files/6/a/1/dataset_6a133926-a50a-4d76-b9cd-ca8b38ca3963.dat'  -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 84
Total scaffold length: 1982895
Average scaffold length: 23605.89
Scaffold N50: 20934
Scaffold auN: 33899.67
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 84
Total contig length: 1982895
Average contig length: 23605.89
Contig N50: 20934
Contig auN: 33899.67
Contig L50: 30
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 606458:383991:386001:606445
GC content %: 38.83
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 84

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp7mwsax3_/files/6/a/1/dataset_6a133926-a50a-4d76-b9cd-ca8b38ca3963.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmp7mwsax3_/job_working_directory/000/17/outputs/dataset_f502036c-933b-45a6-ab07-d1df1effbae1.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp7mwsax3_/files/6/a/1/dataset_6a133926-a50a-4d76-b9cd-ca8b38ca3963.dat' --out-size s   --tabular > '/tmp/tmp7mwsax3_/job_working_directory/000/18/outputs/dataset_6a4f9f48-aec7-41c6-b49c-39dc6a3e0e56.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "s", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp7mwsax3_/files/9/b/1/dataset_9b12fe55-7f0c-4478-bb46-703f9016fda5.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmp7mwsax3_/files/d/3/e/dataset_d3e2e9d9-3014-4a2f-bcd0-865cde644387.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp7mwsax3_/job_working_directory/000/19/outputs/dataset_53391dd6-5b56-4ffb-8d7b-d73d134c5ca6.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 178402556
ref seq len = 3965790
binary seq ticks = 83110179
build suffix-array ticks = 842879943
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 236302426
Total time taken: 0.5606
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 1307277
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000037, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000037 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000053, nseq: 100108
	[0000][ M::kt_pipeline] read 100108 sequences (10000053 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 7.047 CPU sec, 7.569 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000072, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000072 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100108 reads in 6.932 CPU sec, 7.797 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000203, nseq: 100132
	[0000][ M::kt_pipeline] read 100132 sequences (10000203 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 7.537 CPU sec, 9.928 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000073, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000073 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100132 reads in 7.127 CPU sec, 9.116 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000141, nseq: 100166
	[0000][ M::kt_pipeline] read 100166 sequences (10000141 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 6.915 CPU sec, 8.199 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000104, nseq: 118598
	[0000][ M::kt_pipeline] read 118598 sequences (10000104 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100166 reads in 7.304 CPU sec, 9.182 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000109, nseq: 151884
	[0000][ M::kt_pipeline] read 151884 sequences (10000109 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118598 reads in 6.850 CPU sec, 8.363 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000126, nseq: 151908
	[0000][ M::kt_pipeline] read 151908 sequences (10000126 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151884 reads in 6.469 CPU sec, 8.073 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151908 reads in 6.531 CPU sec, 7.848 real sec
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000007, nseq: 151868
	[0000][ M::kt_pipeline] read 151868 sequences (10000007 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 6.462 CPU sec, 7.674 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000077, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000077 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151868 reads in 6.353 CPU sec, 7.744 real sec
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000024, nseq: 127818
	[0000][ M::kt_pipeline] read 127818 sequences (10000024 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 6.353 CPU sec, 7.741 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000071, nseq: 98956
	[0000][ M::kt_pipeline] read 98956 sequences (10000071 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127818 reads in 8.713 CPU sec, 10.756 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000004, nseq: 145156
	[0000][ M::kt_pipeline] read 145156 sequences (10000004 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98956 reads in 10.940 CPU sec, 14.062 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3496096, nseq: 53016
	[0000][ M::kt_pipeline] read 53016 sequences (3496096 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145156 reads in 9.539 CPU sec, 12.023 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 53016 reads in 3.275 CPU sec, 4.375 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.580881 MHz
Runtime profile:

	Time taken for main_mem function: 140.80 sec

	IO times (sec) :
	Reading IO time (reads) avg: 5.86, (5.86, 5.86)
	Writing IO time (SAM) avg: 5.85, (5.85, 5.85)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 140.79
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 140.44, (140.44, 140.44)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 12.26, (12.26, 12.26)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 128.18, (128.18, 128.18)
		SMEM compute avg: 42.17, (42.17, 42.17)
		SAL compute avg: 24.71, (24.71, 24.71)
				MEM_SA avg: 12.78, (12.78, 12.78)

		BSW time, avg: 53.21, (53.21, 53.21)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[1307277] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 2, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 17, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp7mwsax3_/files/9/b/1/dataset_9b12fe55-7f0c-4478-bb46-703f9016fda5.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmp7mwsax3_/files/3/0/9/dataset_309d290e-dc69-4f0e-a822-947568df4cc5.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp7mwsax3_/job_working_directory/000/20/outputs/dataset_0f3482aa-77f2-4f9e-bed8-2a85a8d82929.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 184687664
ref seq len = 3965790
binary seq ticks = 145195080
build suffix-array ticks = 741932391
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 285716924
Total time taken: 0.5861
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 1307277
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000036, nseq: 100212
	[0000][ M::kt_pipeline] read 100212 sequences (10000036 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000140, nseq: 100074
	[0000][ M::kt_pipeline] read 100074 sequences (10000140 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100212 reads in 6.816 CPU sec, 7.800 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000066, nseq: 100106
	[0000][ M::kt_pipeline] read 100106 sequences (10000066 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100074 reads in 7.817 CPU sec, 9.881 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000070, nseq: 100180
	[0000][ M::kt_pipeline] read 100180 sequences (10000070 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100106 reads in 7.366 CPU sec, 9.453 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000000, nseq: 100202
	[0000][ M::kt_pipeline] read 100202 sequences (10000000 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100180 reads in 7.061 CPU sec, 9.065 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000132, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000132 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100202 reads in 7.036 CPU sec, 8.530 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 118588
	[0000][ M::kt_pipeline] read 118588 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 6.935 CPU sec, 8.810 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000125, nseq: 151900
	[0000][ M::kt_pipeline] read 151900 sequences (10000125 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118588 reads in 7.043 CPU sec, 8.567 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000005, nseq: 151874
	[0000][ M::kt_pipeline] read 151874 sequences (10000005 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151900 reads in 6.466 CPU sec, 7.634 real sec
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151904
	[0000][ M::kt_pipeline] read 151904 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151874 reads in 6.107 CPU sec, 7.149 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151896
	[0000][ M::kt_pipeline] read 151896 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151904 reads in 6.377 CPU sec, 7.767 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000130, nseq: 151906
	[0000][ M::kt_pipeline] read 151906 sequences (10000130 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151896 reads in 6.335 CPU sec, 7.251 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 127808
	[0000][ M::kt_pipeline] read 127808 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151906 reads in 6.096 CPU sec, 7.700 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000028, nseq: 98948
	[0000][ M::kt_pipeline] read 98948 sequences (10000028 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127808 reads in 8.268 CPU sec, 10.442 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000026, nseq: 145218
	[0000][ M::kt_pipeline] read 145218 sequences (10000026 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98948 reads in 11.016 CPU sec, 13.858 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3489223, nseq: 52906
	[0000][ M::kt_pipeline] read 52906 sequences (3489223 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145218 reads in 9.444 CPU sec, 11.958 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 52906 reads in 3.124 CPU sec, 3.801 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2446.160213 MHz
Runtime profile:

	Time taken for main_mem function: 139.95 sec

	IO times (sec) :
	Reading IO time (reads) avg: 6.25, (6.25, 6.25)
	Writing IO time (SAM) avg: 5.28, (5.28, 5.28)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 139.94
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 139.63, (139.63, 139.63)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 12.43, (12.43, 12.43)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 127.19, (127.19, 127.19)
		SMEM compute avg: 42.11, (42.11, 42.11)
		SAL compute avg: 24.45, (24.45, 24.45)
				MEM_SA avg: 12.53, (12.53, 12.53)

		BSW time, avg: 53.19, (53.19, 53.19)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[1307277] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 3, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 17, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

busco --in '/tmp/tmp7mwsax3_/files/9/b/1/dataset_9b12fe55-7f0c-4478-bb46-703f9016fda5.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'vertebrata_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific

Exit Code:

```
1
```

Standard Error:

2024-09-24 14:12:35 ERROR:	Something went wrong. Results not recorded.
2024-09-24 14:12:35 ERROR:	BUSCO analysis failed!
2024-09-24 14:12:35 ERROR:	Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

Standard Output:

2024-09-24 13:54:30 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 09/24/2024 13:54:30 *****
2024-09-24 13:54:30 INFO:	Configuring BUSCO with local environment
2024-09-24 13:54:30 INFO:	Running genome mode
2024-09-24 13:54:32 INFO:	Input file is /tmp/tmp7mwsax3_/files/9/b/1/dataset_9b12fe55-7f0c-4478-bb46-703f9016fda5.dat
2024-09-24 13:54:32 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-09-24 13:54:32 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-09-24 13:54:33 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2024-09-24 13:54:33 INFO:	Running 1 job(s) on bbtools, starting at 09/24/2024 13:54:33
2024-09-24 13:54:34 INFO:	[bbtools]	1 of 1 task(s) completed
2024-09-24 13:54:34 INFO:	Running 1 job(s) on miniprot_index, starting at 09/24/2024 13:54:34
2024-09-24 13:54:35 INFO:	[miniprot_index]	1 of 1 task(s) completed
2024-09-24 13:54:35 INFO:	Running 1 job(s) on miniprot_align, starting at 09/24/2024 13:54:35
2024-09-24 14:12:02 INFO:	[miniprot_align]	1 of 1 task(s) completed
2024-09-24 14:12:08 INFO:	***** Run HMMER on gene sequences *****
2024-09-24 14:12:09 INFO:	Running 607 job(s) on hmmsearch, starting at 09/24/2024 14:12:09
2024-09-24 14:12:13 INFO:	[hmmsearch]	61 of 607 task(s) completed
2024-09-24 14:12:16 INFO:	[hmmsearch]	122 of 607 task(s) completed
2024-09-24 14:12:19 INFO:	[hmmsearch]	183 of 607 task(s) completed
2024-09-24 14:12:21 INFO:	[hmmsearch]	243 of 607 task(s) completed
2024-09-24 14:12:23 INFO:	[hmmsearch]	304 of 607 task(s) completed
2024-09-24 14:12:26 INFO:	[hmmsearch]	365 of 607 task(s) completed
2024-09-24 14:12:27 INFO:	[hmmsearch]	425 of 607 task(s) completed
2024-09-24 14:12:29 INFO:	[hmmsearch]	486 of 607 task(s) completed
2024-09-24 14:12:32 INFO:	[hmmsearch]	547 of 607 task(s) completed
2024-09-24 14:12:34 INFO:	[hmmsearch]	607 of 607 task(s) completed
2024-09-24 14:12:35 INFO:	46 exons in total
2024-09-24 14:12:35 WARNING:	2 of 36 Complete matches (5.6%) contain internal stop codons in Miniprot gene predictions
2024-09-24 14:12:35 WARNING:	BUSCO gene predictions from Miniprot have low average identity (0.4699999988079071). You may want to repeat the analysis using the Metaeuk pipeline.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image"]`

Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmp7mwsax3_/job_working_directory/000/22/outputs/dataset_3509b9ea-9950-44be-bd51-6606a6179320.dat' -g     '#' 'Number of' '/tmp/tmp7mwsax3_/files/f/5/0/dataset_f502036c-933b-45a6-ab07-d1df1effbae1.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 30: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp7mwsax3_/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmp7mwsax3_/files/6/a/4/dataset_6a4f9f48-aec7-41c6-b49c-39dc6a3e0e56.dat' --output='/tmp/tmp7mwsax3_/job_working_directory/000/23/outputs/dataset_f9057e37-cbf1-45b3-8acd-05b5763391e7.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"d5d875ff7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp7mwsax3_/job_working_directory/000/24/configs/tmp0odxsfph' '/tmp/tmp7mwsax3_/files/f/9/0/dataset_f9057e37-cbf1-45b3-8acd-05b5763391e7.dat' > '/tmp/tmp7mwsax3_/job_working_directory/000/24/outputs/dataset_615e39e2-9c68-4b69-8dde-b549e55056cc.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875ff7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmp7mwsax3_/files/6/1/5/dataset_615e39e2-9c68-4b69-8dde-b549e55056cc.dat > '/tmp/tmp7mwsax3_/job_working_directory/000/25/outputs/dataset_41f1309a-67ff-404c-9bbb-d44f1c213ab6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875ff7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp7mwsax3_/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp7mwsax3_/files/6/1/5/dataset_615e39e2-9c68-4b69-8dde-b549e55056cc.dat' '/tmp/tmp7mwsax3_/job_working_directory/000/26/outputs/dataset_590e1ae4-8714-44bf-b30e-b2164c19aecf.dat' '1' yes

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875ff7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"d5d875ff7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875ff7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1982895", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmp7mwsax3_/job_working_directory/000/35/configs/tmpgyvjc5or' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp7mwsax3_/files/5/9/0/dataset_590e1ae4-8714-44bf-b30e-b2164c19aecf.dat' '/tmp/tmp7mwsax3_/job_working_directory/000/35/outputs/dataset_a47af878-5605-4470-9c5a-89468332eb70.dat'

Exit Code:

```
0
```

Standard Output:

c3/1982895
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1982895;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 84 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875ff7a7b11ef826c839bb5da03ce"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1982895"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 4: Database for Busco Lineage:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp7mwsax3_/files/5/3/3/dataset_53391dd6-5b56-4ffb-8d7b-d73d134c5ca6.dat' 'forward_input.bam' && ln -s '/tmp/tmp7mwsax3_/files/0/f/3/dataset_0f3482aa-77f2-4f9e-bed8-2a85a8d82929.dat' 'reverse_input.bam' && bellerophon --forward forward_input.bam --reverse reverse_input.bam --quality 20 --output 'merged_out.bam' --threads ${GALAXY_SLOTS:-1} && samtools sort --no-PG -O BAM -o '/tmp/tmp7mwsax3_/job_working_directory/000/28/outputs/dataset_78f4c360-739c-42dd-8108-92638a3b599c.dat' -@ ${GALAXY_SLOTS:-1} merged_out.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 32: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp7mwsax3_/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp7mwsax3_/files/a/4/7/dataset_a47af878-5605-4470-9c5a-89468332eb70.dat' 'c5,c6' T '/tmp/tmp7mwsax3_/job_working_directory/000/36/outputs/dataset_8a516519-8f57-4201-9eee-cec230f253cf.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 33: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp7mwsax3_/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp7mwsax3_/files/a/4/7/dataset_a47af878-5605-4470-9c5a-89468332eb70.dat' 'c4,c7' T '/tmp/tmp7mwsax3_/job_working_directory/000/37/outputs/dataset_491bf0ed-ba51-492c-9ff1-4d0da2d8f4a1.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 34: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmp7mwsax3_/files/7/8/f/dataset_78f4c360-739c-42dd-8108-92638a3b599c.dat' | PretextMap -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 84 sequences, sorted by length, descending. Filtering by minimum mapping quality 10

                                                                                
[PretextMap status] :: 10.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 10.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 15.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 20.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 25.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 30.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 35.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 40.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 45.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 50.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 55.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 60.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 65.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 70.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 75.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 80.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 85.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 90.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 95.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 100.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 105.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 109.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 115.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 120.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 125.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 130.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 135.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 139.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 144.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 150.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 155.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 159.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 165.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 169.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 174.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 179.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 185.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 190.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 195.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 200.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 204.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 210.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 215.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 220.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 224.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 229.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 234.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 239.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 244.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 250.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 255.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 260.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 265.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 270.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 275.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 280.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 285.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 290.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 295.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 300.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 305.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 310.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 315.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 640.0 k reads processed, 320.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 650.0 k reads processed, 325.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 660.0 k reads processed, 330.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 670.0 k reads processed, 335.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 680.0 k reads processed, 340.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 690.0 k reads processed, 345.0 k read-pairs mapped
[PretextMap status] :: Creating MipMaps...
[PretextMap status] :: Equalising contrast...
[PretextMap status] :: Compressing textures...

[PretextMap status] ::   1/528 (0.19%) texture blocks written to disk
[PretextMap status] ::   2/528 (0.38%) texture blocks written to disk
[PretextMap status] ::   3/528 (0.57%) texture blocks written to disk
[PretextMap status] ::   4/528 (0.76%) texture blocks written to disk
[PretextMap status] ::   5/528 (0.95%) texture blocks written to disk
[PretextMap status] ::   6/528 (1.14%) texture blocks written to disk
[PretextMap status] ::   7/528 (1.33%) texture blocks written to disk
[PretextMap status] ::   8/528 (1.52%) texture blocks written to disk
[PretextMap status] ::   9/528 (1.70%) texture blocks written to disk
[PretextMap status] ::  10/528 (1.89%) texture blocks written to disk
[PretextMap status] ::  11/528 (2.08%) texture blocks written to disk
[PretextMap status] ::  12/528 (2.27%) texture blocks written to disk
[PretextMap status] ::  13/528 (2.46%) texture blocks written to disk
[PretextMap status] ::  14/528 (2.65%) texture blocks written to disk
[PretextMap status] ::  15/528 (2.84%) texture blocks written to disk
[PretextMap status] ::  16/528 (3.03%) texture blocks written to disk
[PretextMap status] ::  17/528 (3.22%) texture blocks written to disk
[PretextMap status] ::  18/528 (3.41%) texture blocks written to disk
[PretextMap status] ::  19/528 (3.60%) texture blocks written to disk
[PretextMap status] ::  20/528 (3.79%) texture blocks written to disk
[PretextMap status] ::  21/528 (3.98%) texture blocks written to disk
[PretextMap status] ::  22/528 (4.17%) texture blocks written to disk
[PretextMap status] ::  23/528 (4.36%) texture blocks written to disk
[PretextMap status] ::  24/528 (4.55%) texture blocks written to disk
[PretextMap status] ::  25/528 (4.73%) texture blocks written to disk
[PretextMap status] ::  26/528 (4.92%) texture blocks written to disk
[PretextMap status] ::  27/528 (5.11%) texture blocks written to disk
[PretextMap status] ::  28/528 (5.30%) texture blocks written to disk
[PretextMap status] ::  29/528 (5.49%) texture blocks written to disk
[PretextMap status] ::  30/528 (5.68%) texture blocks written to disk
[PretextMap status] ::  31/528 (5.87%) texture blocks written to disk
[PretextMap status] ::  32/528 (6.06%) texture blocks written to disk
[PretextMap status] ::  33/528 (6.25%) texture blocks written to disk
[PretextMap status] ::  34/528 (6.44%) texture blocks written to disk
[PretextMap status] ::  35/528 (6.63%) texture blocks written to disk
[PretextMap status] ::  36/528 (6.82%) texture blocks written to disk
[PretextMap status] ::  37/528 (7.01%) texture blocks written to disk
[PretextMap status] ::  38/528 (7.20%) texture blocks written to disk
[PretextMap status] ::  39/528 (7.39%) texture blocks written to disk
[PretextMap status] ::  40/528 (7.58%) texture blocks written to disk
[PretextMap status] ::  41/528 (7.77%) texture blocks written to disk
[PretextMap status] ::  42/528 (7.95%) texture blocks written to disk
[PretextMap status] ::  43/528 (8.14%) texture blocks written to disk
[PretextMap status] ::  44/528 (8.33%) texture blocks written to disk
[PretextMap status] ::  45/528 (8.52%) texture blocks written to disk
[PretextMap status] ::  46/528 (8.71%) texture blocks written to disk
[PretextMap status] ::  47/528 (8.90%) texture blocks written to disk
[PretextMap status] ::  48/528 (9.09%) texture blocks written to disk
[PretextMap status] ::  49/528 (9.28%) texture blocks written to disk
[PretextMap status] ::  50/528 (9.47%) texture blocks written to disk
[PretextMap status] ::  51/528 (9.66%) texture blocks written to disk
[PretextMap status] ::  52/528 (9.85%) texture blocks written to disk
[PretextMap status] ::  53/528 (10.04%) texture blocks written to disk
[PretextMap status] ::  54/528 (10.23%) texture blocks written to disk
[PretextMap status] ::  55/528 (10.42%) texture blocks written to disk
[PretextMap status] ::  56/528 (10.61%) texture blocks written to disk
[PretextMap status] ::  57/528 (10.80%) texture blocks written to disk
[PretextMap status] ::  58/528 (10.98%) texture blocks written to disk
[PretextMap status] ::  59/528 (11.17%) texture blocks written to disk
[PretextMap status] ::  60/528 (11.36%) texture blocks written to disk
[PretextMap status] ::  61/528 (11.55%) texture blocks written to disk
[PretextMap status] ::  62/528 (11.74%) texture blocks written to disk
[PretextMap status] ::  63/528 (11.93%) texture blocks written to disk
[PretextMap status] ::  64/528 (12.12%) texture blocks written to disk
[PretextMap status] ::  65/528 (12.31%) texture blocks written to disk
[PretextMap status] ::  66/528 (12.50%) texture blocks written to disk
[PretextMap status] ::  67/528 (12.69%) texture blocks written to disk
[PretextMap status] ::  68/528 (12.88%) texture blocks written to disk
[PretextMap status] ::  69/528 (13.07%) texture blocks written to disk
[PretextMap status] ::  70/528 (13.26%) texture blocks written to disk
[PretextMap status] ::  71/528 (13.45%) texture blocks written to disk
[PretextMap status] ::  72/528 (13.64%) texture blocks written to disk
[PretextMap status] ::  73/528 (13.83%) texture blocks written to disk
[PretextMap status] ::  74/528 (14.02%) texture blocks written to disk
[PretextMap status] ::  75/528 (14.20%) texture blocks written to disk
[PretextMap status] ::  76/528 (14.39%) texture blocks written to disk
[PretextMap status] ::  77/528 (14.58%) texture blocks written to disk
[PretextMap status] ::  78/528 (14.77%) textu
..
:: 298/528 (56.44%) texture blocks written to disk
[PretextMap status] :: 299/528 (56.63%) texture blocks written to disk
[PretextMap status] :: 300/528 (56.82%) texture blocks written to disk
[PretextMap status] :: 301/528 (57.01%) texture blocks written to disk
[PretextMap status] :: 302/528 (57.20%) texture blocks written to disk
[PretextMap status] :: 303/528 (57.39%) texture blocks written to disk
[PretextMap status] :: 304/528 (57.58%) texture blocks written to disk
[PretextMap status] :: 305/528 (57.77%) texture blocks written to disk
[PretextMap status] :: 306/528 (57.95%) texture blocks written to disk
[PretextMap status] :: 307/528 (58.14%) texture blocks written to disk
[PretextMap status] :: 308/528 (58.33%) texture blocks written to disk
[PretextMap status] :: 309/528 (58.52%) texture blocks written to disk
[PretextMap status] :: 310/528 (58.71%) texture blocks written to disk
[PretextMap status] :: 311/528 (58.90%) texture blocks written to disk
[PretextMap status] :: 312/528 (59.09%) texture blocks written to disk
[PretextMap status] :: 313/528 (59.28%) texture blocks written to disk
[PretextMap status] :: 314/528 (59.47%) texture blocks written to disk
[PretextMap status] :: 315/528 (59.66%) texture blocks written to disk
[PretextMap status] :: 316/528 (59.85%) texture blocks written to disk
[PretextMap status] :: 317/528 (60.04%) texture blocks written to disk
[PretextMap status] :: 318/528 (60.23%) texture blocks written to disk
[PretextMap status] :: 319/528 (60.42%) texture blocks written to disk
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Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp7mwsax3_/files/7/8/f/dataset_78f4c360-739c-42dd-8108-92638a3b599c.dat' ./input.bam &&  bedtools bamtobed -bed12   -i ./input.bam > '/tmp/tmp7mwsax3_/job_working_directory/000/30/outputs/dataset_29302a55-7225-4a2a-ac8a-074c054518b1.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ed_score	`false`
option	`"-bed12"`
split	`false`
tag	`""`

Step 36: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp7mwsax3_/job_working_directory/000/38/configs/tmp56hkz9en' && Rscript '/tmp/tmp7mwsax3_/job_working_directory/000/38/configs/tmp56hkz9en'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp7mwsax3_/files/8/a/5/dataset_8a516519-8f57-4201-9eee-cec230f253cf.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp7mwsax3_/job_working_directory/000/38/outputs/dataset_71e734b3-07c2-4769-99a1-49c40e4eca87.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"x"`
xplot	`"1"`
ylab	`"Nx (Mb)"`
yplot	`"2"`

Step 37: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp7mwsax3_/job_working_directory/000/39/configs/tmp8fr5wm6k' && Rscript '/tmp/tmp7mwsax3_/job_working_directory/000/39/configs/tmp8fr5wm6k'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp7mwsax3_/files/4/9/1/dataset_491bf0ed-ba51-492c-9ff1-4d0da2d8f4a1.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp7mwsax3_/job_working_directory/000/39/outputs/dataset_9aaca370-3f01-4715-acdc-e27ce378a264.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"1"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"2"`

Step 38: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmp7mwsax3_/files/4/2/5/dataset_425d6042-fcbd-472a-a706-873dfb6765ce.dat -f png -r 1000 -c 5 --sequences '=full' --minTexels 64 --gridSize 1 --gridColour black '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmp7mwsax3_/files/4/2/5/dataset_425d6042-fcbd-472a-a706-873dfb6765ce.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 1000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 1 pixel
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 0, "gridcolor": "black", "gridsize": "1", "showGrid": "yes"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 39: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

( LC_ALL=C  sort   --stable -t '	'  -k '4,4'  ) < '/tmp/tmp7mwsax3_/files/2/9/3/dataset_29302a55-7225-4a2a-ac8a-074c054518b1.dat' > '/tmp/tmp7mwsax3_/job_working_directory/000/32/outputs/dataset_dc9c9364-f266-497e-af87-491e7b25b909.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
chromInfo	`"/tmp/tmp7mwsax3_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`"0"`
ignore_case	`false`
sortkeys	`[{"__index__": 0, "column": "4", "order": "", "style": ""}]`
unique	`false`

Step 40: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"d5d875fe7a7b11ef826c839bb5da03ce"`
input	`{"values": [{"id": 5, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 5: Lineage:
- step_state: scheduled
Step 6: HiC Forward reads:
- step_state: scheduled
Step 7: HiC reverse reads:
- step_state: scheduled
Step 8: Restriction enzymes:
- step_state: scheduled
Step 9: Estimated genome size - Parameter File:
- step_state: scheduled
Step 10: SAK input file:
- step_state: scheduled

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - af27084b883abc6c
- history_state
  - error
- invocation_id
  - af27084b883abc6c
- invocation_state
  - scheduled
- workflow_id
  - 84d5f4dc2a7e98fe

gxydevbot · 2024-10-14T04:33:07Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-10-14T05:06:00Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input GFA:
- step_state: scheduled
Step 2: Haplotype:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "$&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "hap1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 12: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpdwog5z93/files/a/8/d/dataset_a8d163e2-16d5-4afc-93c3-44c548840186.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 84
Total scaffold length: 1982895
Average scaffold length: 23605.89
Scaffold N50: 20934
Scaffold auN: 33899.67
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 84
Total contig length: 1982895
Average contig length: 23605.89
Contig N50: 20934
Contig auN: 33899.67
Contig L50: 30
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 606458:383991:386001:606445
GC content %: 38.83
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 84
# edges: 4
Average degree: 0.05
# connected components: 1
Largest connected component length: 94650
# dead ends: 165
# disconnected components: 81
Total length disconnected components: 1888245
# separated components: 82
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpdwog5z93/files/9/a/3/dataset_9a3266af-59ba-41a5-9764-bae8f201b3d4.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpdwog5z93/files/6/c/9/dataset_6c964d20-79a2-43d6-8488-35e47f82327d.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpdwog5z93/job_working_directory/000/8/outputs/dataset_5b980386-dc4a-4d93-a621-c6a825ae7478.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 123814719
ref seq len = 3965790
binary seq ticks = 67953720
build suffix-array ticks = 609725149
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 204900164
Total time taken: 0.4228
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 3041008
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000037, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000037 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000053, nseq: 100108
	[0000][ M::kt_pipeline] read 100108 sequences (10000053 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 5.376 CPU sec, 5.379 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000072, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000072 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100108 reads in 5.371 CPU sec, 5.450 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000203, nseq: 100132
	[0000][ M::kt_pipeline] read 100132 sequences (10000203 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 5.490 CPU sec, 5.571 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000073, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000073 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100132 reads in 5.393 CPU sec, 5.480 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000141, nseq: 100166
	[0000][ M::kt_pipeline] read 100166 sequences (10000141 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 5.341 CPU sec, 5.415 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000104, nseq: 118598
	[0000][ M::kt_pipeline] read 118598 sequences (10000104 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100166 reads in 5.532 CPU sec, 5.610 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000109, nseq: 151884
	[0000][ M::kt_pipeline] read 151884 sequences (10000109 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118598 reads in 5.432 CPU sec, 5.521 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000126, nseq: 151908
	[0000][ M::kt_pipeline] read 151908 sequences (10000126 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151884 reads in 5.062 CPU sec, 5.150 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151908 reads in 5.074 CPU sec, 5.186 real sec
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000007, nseq: 151868
	[0000][ M::kt_pipeline] read 151868 sequences (10000007 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 5.046 CPU sec, 5.147 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000077, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000077 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151868 reads in 5.194 CPU sec, 5.289 real sec
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000024, nseq: 127818
	[0000][ M::kt_pipeline] read 127818 sequences (10000024 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 5.175 CPU sec, 5.278 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000071, nseq: 98956
	[0000][ M::kt_pipeline] read 98956 sequences (10000071 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127818 reads in 6.730 CPU sec, 6.832 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000004, nseq: 145156
	[0000][ M::kt_pipeline] read 145156 sequences (10000004 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98956 reads in 8.629 CPU sec, 8.722 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3496096, nseq: 53016
	[0000][ M::kt_pipeline] read 53016 sequences (3496096 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145156 reads in 7.613 CPU sec, 7.697 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 53016 reads in 2.690 CPU sec, 2.785 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.584414 MHz
Runtime profile:

	Time taken for main_mem function: 90.71 sec

	IO times (sec) :
	Reading IO time (reads) avg: 5.05, (5.05, 5.05)
	Writing IO time (SAM) avg: 3.86, (3.86, 3.86)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.00, (0.00, 0.00)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 90.70
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 90.51, (90.51, 90.51)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 7.74, (7.74, 7.74)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 82.76, (82.76, 82.76)
		SMEM compute avg: 27.52, (27.52, 27.52)
		SAL compute avg: 17.37, (17.37, 17.37)
				MEM_SA avg: 8.97, (8.97, 8.97)

		BSW time, avg: 32.64, (32.64, 32.64)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[3041008] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 2, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 7, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpdwog5z93/files/9/a/3/dataset_9a3266af-59ba-41a5-9764-bae8f201b3d4.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpdwog5z93/files/3/3/9/dataset_339d9682-6138-45d5-a6fd-7ffe8e06b684.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpdwog5z93/job_working_directory/000/9/outputs/dataset_2383f7a3-1cdc-4032-a0a4-fac2cca387d4.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 126223412
ref seq len = 3965790
binary seq ticks = 70164468
build suffix-array ticks = 616847035
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 210485544
Total time taken: 0.4322
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 3041008
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000036, nseq: 100212
	[0000][ M::kt_pipeline] read 100212 sequences (10000036 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000140, nseq: 100074
	[0000][ M::kt_pipeline] read 100074 sequences (10000140 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100212 reads in 5.506 CPU sec, 5.507 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000066, nseq: 100106
	[0000][ M::kt_pipeline] read 100106 sequences (10000066 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100074 reads in 5.506 CPU sec, 5.572 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000070, nseq: 100180
	[0000][ M::kt_pipeline] read 100180 sequences (10000070 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100106 reads in 5.505 CPU sec, 5.579 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000000, nseq: 100202
	[0000][ M::kt_pipeline] read 100202 sequences (10000000 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100180 reads in 5.445 CPU sec, 5.522 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000132, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000132 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100202 reads in 5.416 CPU sec, 5.495 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 118588
	[0000][ M::kt_pipeline] read 118588 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 5.472 CPU sec, 5.555 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000125, nseq: 151900
	[0000][ M::kt_pipeline] read 151900 sequences (10000125 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118588 reads in 5.574 CPU sec, 5.648 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000005, nseq: 151874
	[0000][ M::kt_pipeline] read 151874 sequences (10000005 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151900 reads in 5.106 CPU sec, 5.192 real sec
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151904
	[0000][ M::kt_pipeline] read 151904 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151874 reads in 5.103 CPU sec, 5.198 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151896
	[0000][ M::kt_pipeline] read 151896 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151904 reads in 5.062 CPU sec, 5.164 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000130, nseq: 151906
	[0000][ M::kt_pipeline] read 151906 sequences (10000130 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151896 reads in 5.090 CPU sec, 5.190 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 127808
	[0000][ M::kt_pipeline] read 127808 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151906 reads in 5.154 CPU sec, 5.237 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000028, nseq: 98948
	[0000][ M::kt_pipeline] read 98948 sequences (10000028 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127808 reads in 6.659 CPU sec, 6.754 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000026, nseq: 145218
	[0000][ M::kt_pipeline] read 145218 sequences (10000026 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98948 reads in 8.906 CPU sec, 8.992 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3489223, nseq: 52906
	[0000][ M::kt_pipeline] read 52906 sequences (3489223 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145218 reads in 7.657 CPU sec, 7.738 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 52906 reads in 2.714 CPU sec, 2.800 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.575202 MHz
Runtime profile:

	Time taken for main_mem function: 91.37 sec

	IO times (sec) :
	Reading IO time (reads) avg: 5.28, (5.28, 5.28)
	Writing IO time (SAM) avg: 3.67, (3.67, 3.67)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.00, (0.00, 0.00)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 91.36
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 91.14, (91.14, 91.14)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 8.45, (8.45, 8.45)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 82.69, (82.69, 82.69)
		SMEM compute avg: 28.23, (28.23, 28.23)
		SAL compute avg: 17.21, (17.21, 17.21)
				MEM_SA avg: 9.08, (9.08, 9.08)

		BSW time, avg: 32.48, (32.48, 32.48)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[3041008] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 3, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 7, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpdwog5z93/files/5/b/9/dataset_5b980386-dc4a-4d93-a621-c6a825ae7478.dat' 'forward_input.bam' && ln -s '/tmp/tmpdwog5z93/files/2/3/8/dataset_2383f7a3-1cdc-4032-a0a4-fac2cca387d4.dat' 'reverse_input.bam' && bellerophon --forward forward_input.bam --reverse reverse_input.bam --quality 20 --output 'merged_out.bam' --threads ${GALAXY_SLOTS:-1} && samtools sort --no-PG -O BAM -o '/tmp/tmpdwog5z93/job_working_directory/000/10/outputs/dataset_0853d51b-b08b-4238-9887-1fc996e795d6.dat' -@ ${GALAXY_SLOTS:-1} merged_out.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmpdwog5z93/files/0/8/5/dataset_0853d51b-b08b-4238-9887-1fc996e795d6.dat' | PretextMap -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 84 sequences, sorted by length, descending. Filtering by minimum mapping quality 10

                                                                                
[PretextMap status] :: 10.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 10.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 15.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 20.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 25.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 30.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 35.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 40.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 45.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 50.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 55.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 60.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 65.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 70.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 75.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 80.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 85.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 90.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 95.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 100.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 104.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 109.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 114.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 119.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 124.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 129.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 134.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 139.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 145.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 150.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 154.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 159.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 165.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 170.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 175.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 180.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 185.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 190.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 195.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 200.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 205.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 210.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 215.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 220.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 225.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 230.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 235.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 240.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 245.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 250.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 255.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 260.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 265.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 270.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 275.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 280.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 285.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 290.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 295.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 300.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 305.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 310.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 315.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 640.0 k reads processed, 320.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 650.0 k reads processed, 325.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 660.0 k reads processed, 330.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 670.0 k reads processed, 335.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 680.0 k reads processed, 340.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 690.0 k reads processed, 345.0 k read-pairs mapped
[PretextMap status] :: Creating MipMaps...
[PretextMap status] :: Equalising contrast...
[PretextMap status] :: Compressing textures...

[PretextMap status] ::   1/528 (0.19%) texture blocks written to disk
[PretextMap status] ::   2/528 (0.38%) texture blocks written to disk
[PretextMap status] ::   3/528 (0.57%) texture blocks written to disk
[PretextMap status] ::   4/528 (0.76%) texture blocks written to disk
[PretextMap status] ::   5/528 (0.95%) texture blocks written to disk
[PretextMap status] ::   6/528 (1.14%) texture blocks written to disk
[PretextMap status] ::   7/528 (1.33%) texture blocks written to disk
[PretextMap status] ::   8/528 (1.52%) texture blocks written to disk
[PretextMap status] ::   9/528 (1.70%) texture blocks written to disk
[PretextMap status] ::  10/528 (1.89%) texture blocks written to disk
[PretextMap status] ::  11/528 (2.08%) texture blocks written to disk
[PretextMap status] ::  12/528 (2.27%) texture blocks written to disk
[PretextMap status] ::  13/528 (2.46%) texture blocks written to disk
[PretextMap status] ::  14/528 (2.65%) texture blocks written to disk
[PretextMap status] ::  15/528 (2.84%) texture blocks written to disk
[PretextMap status] ::  16/528 (3.03%) texture blocks written to disk
[PretextMap status] ::  17/528 (3.22%) texture blocks written to disk
[PretextMap status] ::  18/528 (3.41%) texture blocks written to disk
[PretextMap status] ::  19/528 (3.60%) texture blocks written to disk
[PretextMap status] ::  20/528 (3.79%) texture blocks written to disk
[PretextMap status] ::  21/528 (3.98%) texture blocks written to disk
[PretextMap status] ::  22/528 (4.17%) texture blocks written to disk
[PretextMap status] ::  23/528 (4.36%) texture blocks written to disk
[PretextMap status] ::  24/528 (4.55%) texture blocks written to disk
[PretextMap status] ::  25/528 (4.73%) texture blocks written to disk
[PretextMap status] ::  26/528 (4.92%) texture blocks written to disk
[PretextMap status] ::  27/528 (5.11%) texture blocks written to disk
[PretextMap status] ::  28/528 (5.30%) texture blocks written to disk
[PretextMap status] ::  29/528 (5.49%) texture blocks written to disk
[PretextMap status] ::  30/528 (5.68%) texture blocks written to disk
[PretextMap status] ::  31/528 (5.87%) texture blocks written to disk
[PretextMap status] ::  32/528 (6.06%) texture blocks written to disk
[PretextMap status] ::  33/528 (6.25%) texture blocks written to disk
[PretextMap status] ::  34/528 (6.44%) texture blocks written to disk
[PretextMap status] ::  35/528 (6.63%) texture blocks written to disk
[PretextMap status] ::  36/528 (6.82%) texture blocks written to disk
[PretextMap status] ::  37/528 (7.01%) texture blocks written to disk
[PretextMap status] ::  38/528 (7.20%) texture blocks written to disk
[PretextMap status] ::  39/528 (7.39%) texture blocks written to disk
[PretextMap status] ::  40/528 (7.58%) texture blocks written to disk
[PretextMap status] ::  41/528 (7.77%) texture blocks written to disk
[PretextMap status] ::  42/528 (7.95%) texture blocks written to disk
[PretextMap status] ::  43/528 (8.14%) texture blocks written to disk
[PretextMap status] ::  44/528 (8.33%) texture blocks written to disk
[PretextMap status] ::  45/528 (8.52%) texture blocks written to disk
[PretextMap status] ::  46/528 (8.71%) texture blocks written to disk
[PretextMap status] ::  47/528 (8.90%) texture blocks written to disk
[PretextMap status] ::  48/528 (9.09%) texture blocks written to disk
[PretextMap status] ::  49/528 (9.28%) texture blocks written to disk
[PretextMap status] ::  50/528 (9.47%) texture blocks written to disk
[PretextMap status] ::  51/528 (9.66%) texture blocks written to disk
[PretextMap status] ::  52/528 (9.85%) texture blocks written to disk
[PretextMap status] ::  53/528 (10.04%) texture blocks written to disk
[PretextMap status] ::  54/528 (10.23%) texture blocks written to disk
[PretextMap status] ::  55/528 (10.42%) texture blocks written to disk
[PretextMap status] ::  56/528 (10.61%) texture blocks written to disk
[PretextMap status] ::  57/528 (10.80%) texture blocks written to disk
[PretextMap status] ::  58/528 (10.98%) texture blocks written to disk
[PretextMap status] ::  59/528 (11.17%) texture blocks written to disk
[PretextMap status] ::  60/528 (11.36%) texture blocks written to disk
[PretextMap status] ::  61/528 (11.55%) texture blocks written to disk
[PretextMap status] ::  62/528 (11.74%) texture blocks written to disk
[PretextMap status] ::  63/528 (11.93%) texture blocks written to disk
[PretextMap status] ::  64/528 (12.12%) texture blocks written to disk
[PretextMap status] ::  65/528 (12.31%) texture blocks written to disk
[PretextMap status] ::  66/528 (12.50%) texture blocks written to disk
[PretextMap status] ::  67/528 (12.69%) texture blocks written to disk
[PretextMap status] ::  68/528 (12.88%) texture blocks written to disk
[PretextMap status] ::  69/528 (13.07%) texture blocks written to disk
[PretextMap status] ::  70/528 (13.26%) texture blocks written to disk
[PretextMap status] ::  71/528 (13.45%) texture blocks written to disk
[PretextMap status] ::  72/528 (13.64%) texture blocks written to disk
[PretextMap status] ::  73/528 (13.83%) texture blocks written to disk
[PretextMap status] ::  74/528 (14.02%) texture blocks written to disk
[PretextMap status] ::  75/528 (14.20%) texture blocks written to disk
[PretextMap status] ::  76/528 (14.39%) texture blocks written to disk
[PretextMap status] ::  77/528 (14.58%) texture blocks written to disk
[PretextMap status] ::  78/528 (14.77%) textu
..
:: 298/528 (56.44%) texture blocks written to disk
[PretextMap status] :: 299/528 (56.63%) texture blocks written to disk
[PretextMap status] :: 300/528 (56.82%) texture blocks written to disk
[PretextMap status] :: 301/528 (57.01%) texture blocks written to disk
[PretextMap status] :: 302/528 (57.20%) texture blocks written to disk
[PretextMap status] :: 303/528 (57.39%) texture blocks written to disk
[PretextMap status] :: 304/528 (57.58%) texture blocks written to disk
[PretextMap status] :: 305/528 (57.77%) texture blocks written to disk
[PretextMap status] :: 306/528 (57.95%) texture blocks written to disk
[PretextMap status] :: 307/528 (58.14%) texture blocks written to disk
[PretextMap status] :: 308/528 (58.33%) texture blocks written to disk
[PretextMap status] :: 309/528 (58.52%) texture blocks written to disk
[PretextMap status] :: 310/528 (58.71%) texture blocks written to disk
[PretextMap status] :: 311/528 (58.90%) texture blocks written to disk
[PretextMap status] :: 312/528 (59.09%) texture blocks written to disk
[PretextMap status] :: 313/528 (59.28%) texture blocks written to disk
[PretextMap status] :: 314/528 (59.47%) texture blocks written to disk
[PretextMap status] :: 315/528 (59.66%) texture blocks written to disk
[PretextMap status] :: 316/528 (59.85%) texture blocks written to disk
[PretextMap status] :: 317/528 (60.04%) texture blocks written to disk
[PretextMap status] :: 318/528 (60.23%) texture blocks written to disk
[PretextMap status] :: 319/528 (60.42%) texture blocks written to disk
[PretextMap status] :: 320/528 (60.61%) texture blocks written to disk
[PretextMap status] :: 321/528 (60.80%) texture blocks written to disk
[PretextMap status] :: 322/528 (60.98%) texture blocks written to disk
[PretextMap status] :: 323/528 (61.17%) texture blocks written to disk
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[PretextMap status] :: 528/528 (100.00%) texture blocks written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpdwog5z93/files/9/a/3/dataset_9a3266af-59ba-41a5-9764-bae8f201b3d4.dat' input.fasta && ln -s '/tmp/tmpdwog5z93/files/0/8/5/dataset_0853d51b-b08b-4238-9887-1fc996e795d6.dat' input.bam && samtools faidx input.fasta && mkdir initial_break agp_out agp_break final_outs && yahs --no-mem-check input.fasta input.bam -e 'GATC,GANTC,CTNAG,TTAA' --no-contig-ec  -o yahs_out 2> output.log && ls -lah && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/yahs/ff4031bfaa22/yahs/move_files.py' && ls -lah ./*

Exit Code:

```
0
```

Standard Output:

total 8M     
drwxr-xr-x    6 1001     118         4.0K Oct 14 04:44 .
drwxr-xr-x   12 1001     118         4.0K Oct 14 04:44 ..
drwxr-xr-x    2 1001     118         4.0K Oct 14 04:44 agp_break
drwxr-xr-x    2 1001     118         4.0K Oct 14 04:44 agp_out
drwxr-xr-x    2 1001     118         4.0K Oct 14 04:44 final_outs
drwxr-xr-x    2 1001     118         4.0K Oct 14 04:44 initial_break
lrwxrwxrwx    1 1001     118           77 Oct 14 04:44 input.bam -> /tmp/tmpdwog5z93/files/0/8/5/dataset_0853d51b-b08b-4238-9887-1fc996e795d6.dat
lrwxrwxrwx    1 1001     118           77 Oct 14 04:44 input.fasta -> /tmp/tmpdwog5z93/files/9/a/3/dataset_9a3266af-59ba-41a5-9764-bae8f201b3d4.dat
-rw-r--r--    1 1001     118         3.5K Oct 14 04:44 input.fasta.fai
-rw-r--r--    1 1001     118         5.1K Oct 14 04:44 output.log
-rw-r--r--    1 1001     118         5.6M Oct 14 04:44 yahs_out.bin
-rw-r--r--    1 1001     118         4.2K Oct 14 04:44 yahs_out_no_break.agp
-rw-r--r--    1 1001     118         4.2K Oct 14 04:44 yahs_out_scaffolds_final.agp
-rw-r--r--    1 1001     118         1.9M Oct 14 04:44 yahs_out_scaffolds_final.fa
lrwxrwxrwx    1 1001     118           77 Oct 14 04:44 ./input.bam -> /tmp/tmpdwog5z93/files/0/8/5/dataset_0853d51b-b08b-4238-9887-1fc996e795d6.dat
lrwxrwxrwx    1 1001     118           77 Oct 14 04:44 ./input.fasta -> /tmp/tmpdwog5z93/files/9/a/3/dataset_9a3266af-59ba-41a5-9764-bae8f201b3d4.dat
-rw-r--r--    1 1001     118         3.5K Oct 14 04:44 ./input.fasta.fai
-rw-r--r--    1 1001     118         5.1K Oct 14 04:44 ./output.log
-rw-r--r--    1 1001     118         5.6M Oct 14 04:44 ./yahs_out.bin

./agp_break:
total 16K    
drwxr-xr-x    2 1001     118         4.0K Oct 14 04:44 .
drwxr-xr-x    6 1001     118         4.0K Oct 14 04:44 ..
-rw-r--r--    1 1001     118         4.2K Oct 14 04:44 yahs_out_no_break.agp

./agp_out:
total 8K     
drwxr-xr-x    2 1001     118         4.0K Oct 14 04:44 .
drwxr-xr-x    6 1001     118         4.0K Oct 14 04:44 ..

./final_outs:
total 2M     
drwxr-xr-x    2 1001     118         4.0K Oct 14 04:44 .
drwxr-xr-x    6 1001     118         4.0K Oct 14 04:44 ..
-rw-r--r--    1 1001     118         4.2K Oct 14 04:44 yahs_out_scaffolds_final.agp
-rw-r--r--    1 1001     118         1.9M Oct 14 04:44 yahs_out_scaffolds_final.fa

./initial_break:
total 8K     
drwxr-xr-x    2 1001     118         4.0K Oct 14 04:44 .
drwxr-xr-x    6 1001     118         4.0K Oct 14 04:44 ..

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function	`{"__current_case__": 0, "agp": null, "bfile": {"values": [{"id": 10, "src": "hda"}]}, "enzyme_conditional": {"__current_case__": 1, "enzyme_options": "preconfigured", "preconfigured_enzymes": "arima2"}, "fasta": {"values": [{"id": 7, "src": "hda"}]}, "function_select": "yahs", "length": null, "no_contig_ec": true, "no_scaffold_ec": false, "quality": null, "res": ""}`
log_out	`true`

Step 19: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmpdwog5z93/files/8/6/1/dataset_86167a4c-d603-4fd3-80fd-289019a963e9.dat -f png -r 1000 -c 5 --sequences '=full' --minTexels 64 --gridSize 0 '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmpdwog5z93/files/8/6/1/dataset_86167a4c-d603-4fd3-80fd-289019a963e9.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 1000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 0 pixels
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 1, "showGrid": "no"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmpdwog5z93/job_working_directory/000/14/outputs/dataset_4f6cf614-bb4f-48ee-b412-d76ca03bf9d4.dat' -g  -w  -r 'scaffold_[0-9]*' '$&.hap1' '/tmp/tmpdwog5z93/files/5/9/1/dataset_591743e4-4912-4bec-9931-db2f35a66207.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "scaffold_[0-9]*", "global": true, "is_regex": true, "replace_pattern": "$&.hap1", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": true}]`

Step 3: Sequence graph:
- step_state: scheduled

Step 21: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpdwog5z93/files/9/a/3/dataset_9a3266af-59ba-41a5-9764-bae8f201b3d4.dat' --agp-to-path /tmp/tmpdwog5z93/files/4/f/6/dataset_4f6cf614-bb4f-48ee-b412-d76ca03bf9d4.dat  -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 83
Total scaffold length: 1971489
Average scaffold length: 23752.88
Scaffold N50: 20934
Scaffold auN: 34029.81
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11828
# contigs: 83
Total contig length: 1971489
Average contig length: 23752.88
Contig N50: 20934
Contig auN: 34029.81
Contig L50: 30
Largest contig: 132632
Smallest contig: 11828
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 603206:382062:383274:602947
GC content %: 38.82
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 83

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 2, "agp_to_path": {"values": [{"id": 15, "src": "hda"}]}, "discover_paths": false, "selector": "scaffolding"}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpdwog5z93/files/0/b/c/dataset_0bcc17f6-9c6f-4e90-8521-83e5a13e9256.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 83
Total scaffold length: 1971489
Average scaffold length: 23752.88
Scaffold N50: 20934
Scaffold auN: 34029.81
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11828
# contigs: 83
Total contig length: 1971489
Average contig length: 23752.88
Contig N50: 20934
Contig auN: 34029.81
Contig L50: 30
Largest contig: 132632
Smallest contig: 11828
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 603206:382062:383274:602947
GC content %: 38.82
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 83

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpdwog5z93/files/0/b/c/dataset_0bcc17f6-9c6f-4e90-8521-83e5a13e9256.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmpdwog5z93/job_working_directory/000/17/outputs/dataset_05d74f6a-5616-4916-ba3d-11cf19bff802.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpdwog5z93/files/0/b/c/dataset_0bcc17f6-9c6f-4e90-8521-83e5a13e9256.dat' --out-size s   --tabular > '/tmp/tmpdwog5z93/job_working_directory/000/18/outputs/dataset_06f857f7-f7fd-4b2f-b86e-cf0defb1f5b1.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "s", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpdwog5z93/files/8/9/0/dataset_89082e19-c92b-490b-a14f-23f0986bce5a.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpdwog5z93/files/6/c/9/dataset_6c964d20-79a2-43d6-8488-35e47f82327d.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpdwog5z93/job_working_directory/000/19/outputs/dataset_acdbe52d-d41b-4afa-bbb8-821138ed527b.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 172607694
ref seq len = 3942978
binary seq ticks = 70169397
build suffix-array ticks = 663674007
pos: 492873, ref_seq_len__: 492872
build fm-index ticks = 205637565
Total time taken: 0.4684
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3942979
* sentinel-index: 3258568
* Count:
0,	1
1,	1206154
2,	1971490
3,	2736826
4,	3942979

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3942978 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000037, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000037 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000053, nseq: 100108
	[0000][ M::kt_pipeline] read 100108 sequences (10000053 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 6.842 CPU sec, 7.252 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000072, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000072 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100108 reads in 7.330 CPU sec, 8.102 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000203, nseq: 100132
	[0000][ M::kt_pipeline] read 100132 sequences (10000203 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 7.205 CPU sec, 7.723 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000073, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000073 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100132 reads in 7.462 CPU sec, 8.457 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000141, nseq: 100166
	[0000][ M::kt_pipeline] read 100166 sequences (10000141 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 7.398 CPU sec, 8.363 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000104, nseq: 118598
	[0000][ M::kt_pipeline] read 118598 sequences (10000104 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100166 reads in 7.396 CPU sec, 8.444 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000109, nseq: 151884
	[0000][ M::kt_pipeline] read 151884 sequences (10000109 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118598 reads in 7.142 CPU sec, 8.010 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000126, nseq: 151908
	[0000][ M::kt_pipeline] read 151908 sequences (10000126 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151884 reads in 6.743 CPU sec, 7.843 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151908 reads in 6.905 CPU sec, 8.185 real sec
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000007, nseq: 151868
	[0000][ M::kt_pipeline] read 151868 sequences (10000007 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 6.749 CPU sec, 7.570 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000077, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000077 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151868 reads in 6.734 CPU sec, 7.820 real sec
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000024, nseq: 127818
	[0000][ M::kt_pipeline] read 127818 sequences (10000024 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 6.502 CPU sec, 8.003 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000071, nseq: 98956
	[0000][ M::kt_pipeline] read 98956 sequences (10000071 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127818 reads in 8.589 CPU sec, 10.589 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000004, nseq: 145156
	[0000][ M::kt_pipeline] read 145156 sequences (10000004 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98956 reads in 11.118 CPU sec, 13.659 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3496096, nseq: 53016
	[0000][ M::kt_pipeline] read 53016 sequences (3496096 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145156 reads in 9.603 CPU sec, 12.078 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 53016 reads in 3.293 CPU sec, 3.624 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.568685 MHz
Runtime profile:

	Time taken for main_mem function: 136.15 sec

	IO times (sec) :
	Reading IO time (reads) avg: 6.04, (6.04, 6.04)
	Writing IO time (SAM) avg: 5.08, (5.08, 5.08)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 136.14
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 135.72, (135.72, 135.72)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 11.81, (11.81, 11.81)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 123.91, (123.91, 123.91)
		SMEM compute avg: 42.87, (42.87, 42.87)
		SAL compute avg: 23.87, (23.87, 23.87)
				MEM_SA avg: 12.57, (12.57, 12.57)

		BSW time, avg: 49.54, (49.54, 49.54)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3942978
count = 0, 1206153, 1971489, 2736825, 3942978
BWT[3258568] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61609

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 2, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 17, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpdwog5z93/files/8/9/0/dataset_89082e19-c92b-490b-a14f-23f0986bce5a.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpdwog5z93/files/3/3/9/dataset_339d9682-6138-45d5-a6fd-7ffe8e06b684.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpdwog5z93/job_working_directory/000/20/outputs/dataset_b125d42c-4cac-4761-97b3-a8b05b851af9.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 166500187
ref seq len = 3942978
binary seq ticks = 82340868
build suffix-array ticks = 940896922
pos: 492873, ref_seq_len__: 492872
build fm-index ticks = 295158855
Total time taken: 0.6291
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3942979
* sentinel-index: 3258568
* Count:
0,	1
1,	1206154
2,	1971490
3,	2736826
4,	3942979

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3942978 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000036, nseq: 100212
	[0000][ M::kt_pipeline] read 100212 sequences (10000036 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000140, nseq: 100074
	[0000][ M::kt_pipeline] read 100074 sequences (10000140 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100212 reads in 7.503 CPU sec, 8.822 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000066, nseq: 100106
	[0000][ M::kt_pipeline] read 100106 sequences (10000066 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100074 reads in 7.645 CPU sec, 8.891 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000070, nseq: 100180
	[0000][ M::kt_pipeline] read 100180 sequences (10000070 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100106 reads in 7.673 CPU sec, 8.880 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000000, nseq: 100202
	[0000][ M::kt_pipeline] read 100202 sequences (10000000 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100180 reads in 7.443 CPU sec, 8.565 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000132, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000132 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100202 reads in 7.464 CPU sec, 8.616 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 118588
	[0000][ M::kt_pipeline] read 118588 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 7.387 CPU sec, 8.673 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000125, nseq: 151900
	[0000][ M::kt_pipeline] read 151900 sequences (10000125 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118588 reads in 7.244 CPU sec, 8.232 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000005, nseq: 151874
	[0000][ M::kt_pipeline] read 151874 sequences (10000005 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151900 reads in 6.572 CPU sec, 7.673 real sec
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151904
	[0000][ M::kt_pipeline] read 151904 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151874 reads in 6.264 CPU sec, 7.881 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151896
	[0000][ M::kt_pipeline] read 151896 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151904 reads in 6.224 CPU sec, 7.888 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000130, nseq: 151906
	[0000][ M::kt_pipeline] read 151906 sequences (10000130 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151896 reads in 6.238 CPU sec, 7.582 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 127808
	[0000][ M::kt_pipeline] read 127808 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151906 reads in 6.122 CPU sec, 7.618 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000028, nseq: 98948
	[0000][ M::kt_pipeline] read 98948 sequences (10000028 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127808 reads in 8.368 CPU sec, 10.132 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000026, nseq: 145218
	[0000][ M::kt_pipeline] read 145218 sequences (10000026 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98948 reads in 11.278 CPU sec, 11.966 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3489223, nseq: 52906
	[0000][ M::kt_pipeline] read 52906 sequences (3489223 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145218 reads in 9.369 CPU sec, 9.861 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 52906 reads in 3.237 CPU sec, 3.385 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2451.344897 MHz
Runtime profile:

	Time taken for main_mem function: 134.70 sec

	IO times (sec) :
	Reading IO time (reads) avg: 5.94, (5.94, 5.94)
	Writing IO time (SAM) avg: 4.67, (4.67, 4.67)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 134.69
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 134.34, (134.34, 134.34)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 11.74, (11.74, 11.74)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 122.60, (122.60, 122.60)
		SMEM compute avg: 42.67, (42.67, 42.67)
		SAL compute avg: 23.17, (23.17, 23.17)
				MEM_SA avg: 12.15, (12.15, 12.15)

		BSW time, avg: 49.59, (49.59, 49.59)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3942978
count = 0, 1206153, 1971489, 2736825, 3942978
BWT[3258568] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61609

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 3, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 17, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

busco --in '/tmp/tmpdwog5z93/files/8/9/0/dataset_89082e19-c92b-490b-a14f-23f0986bce5a.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'vertebrata_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific

Exit Code:

```
1
```

Standard Error:

2024-10-14 05:04:45 ERROR:	Something went wrong. Results not recorded.
2024-10-14 05:04:45 ERROR:	BUSCO analysis failed!
2024-10-14 05:04:45 ERROR:	Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

Standard Output:

2024-10-14 04:46:04 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 10/14/2024 04:46:04 *****
2024-10-14 04:46:04 INFO:	Configuring BUSCO with local environment
2024-10-14 04:46:04 INFO:	Running genome mode
2024-10-14 04:46:07 INFO:	Input file is /tmp/tmpdwog5z93/files/8/9/0/dataset_89082e19-c92b-490b-a14f-23f0986bce5a.dat
2024-10-14 04:46:07 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-10-14 04:46:07 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-10-14 04:46:07 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2024-10-14 04:46:07 INFO:	Running 1 job(s) on bbtools, starting at 10/14/2024 04:46:07
2024-10-14 04:46:09 INFO:	[bbtools]	1 of 1 task(s) completed
2024-10-14 04:46:09 INFO:	Running 1 job(s) on miniprot_index, starting at 10/14/2024 04:46:09
2024-10-14 04:46:10 INFO:	[miniprot_index]	1 of 1 task(s) completed
2024-10-14 04:46:10 INFO:	Running 1 job(s) on miniprot_align, starting at 10/14/2024 04:46:10
2024-10-14 05:03:34 INFO:	[miniprot_align]	1 of 1 task(s) completed
2024-10-14 05:03:39 INFO:	***** Run HMMER on gene sequences *****
2024-10-14 05:03:41 INFO:	Running 607 job(s) on hmmsearch, starting at 10/14/2024 05:03:41
2024-10-14 05:03:49 INFO:	[hmmsearch]	61 of 607 task(s) completed
2024-10-14 05:03:55 INFO:	[hmmsearch]	122 of 607 task(s) completed
2024-10-14 05:04:02 INFO:	[hmmsearch]	183 of 607 task(s) completed
2024-10-14 05:04:07 INFO:	[hmmsearch]	243 of 607 task(s) completed
2024-10-14 05:04:14 INFO:	[hmmsearch]	304 of 607 task(s) completed
2024-10-14 05:04:20 INFO:	[hmmsearch]	365 of 607 task(s) completed
2024-10-14 05:04:26 INFO:	[hmmsearch]	425 of 607 task(s) completed
2024-10-14 05:04:32 INFO:	[hmmsearch]	486 of 607 task(s) completed
2024-10-14 05:04:38 INFO:	[hmmsearch]	547 of 607 task(s) completed
2024-10-14 05:04:45 INFO:	[hmmsearch]	607 of 607 task(s) completed
2024-10-14 05:04:45 INFO:	46 exons in total
2024-10-14 05:04:45 WARNING:	2 of 36 Complete matches (5.6%) contain internal stop codons in Miniprot gene predictions
2024-10-14 05:04:45 WARNING:	BUSCO gene predictions from Miniprot have low average identity (0.4699999988079071). You may want to repeat the analysis using the Metaeuk pipeline.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image"]`

Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmpdwog5z93/job_working_directory/000/22/outputs/dataset_1e7a9096-1ee5-453f-b8af-91240c8b2614.dat' -g     '#' 'Number of' '/tmp/tmpdwog5z93/files/0/5/d/dataset_05d74f6a-5616-4916-ba3d-11cf19bff802.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 30: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpdwog5z93/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmpdwog5z93/files/0/6/f/dataset_06f857f7-f7fd-4b2f-b86e-cf0defb1f5b1.dat' --output='/tmp/tmpdwog5z93/job_working_directory/000/23/outputs/dataset_e20b2a3b-6a89-451d-812b-3d1a8f19d3ed.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6f6d0e7d89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpdwog5z93/job_working_directory/000/24/configs/tmptouso87z' '/tmp/tmpdwog5z93/files/e/2/0/dataset_e20b2a3b-6a89-451d-812b-3d1a8f19d3ed.dat' > '/tmp/tmpdwog5z93/job_working_directory/000/24/outputs/dataset_9a67ae5e-699b-42fe-ab40-0a93155990cb.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7d89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmpdwog5z93/files/9/a/6/dataset_9a67ae5e-699b-42fe-ab40-0a93155990cb.dat > '/tmp/tmpdwog5z93/job_working_directory/000/25/outputs/dataset_4855d22e-0736-411e-8edb-0103deb607ef.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7d89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpdwog5z93/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpdwog5z93/files/9/a/6/dataset_9a67ae5e-699b-42fe-ab40-0a93155990cb.dat' '/tmp/tmpdwog5z93/job_working_directory/000/26/outputs/dataset_94464ec6-77b4-4aa9-9988-1e42ef82f85c.dat' '1' yes

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7d89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6f6d0e7d89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7d89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1971489", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmpdwog5z93/job_working_directory/000/35/configs/tmpb3tsjrj2' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpdwog5z93/files/9/4/4/dataset_94464ec6-77b4-4aa9-9988-1e42ef82f85c.dat' '/tmp/tmpdwog5z93/job_working_directory/000/35/outputs/dataset_34deabee-d8ac-48f9-8f94-e42e0291ab31.dat'

Exit Code:

```
0
```

Standard Output:

c3/1971489
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1971489;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 83 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7d89e611efb6216045bd0674c9"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1971489"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 4: Database for Busco Lineage:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpdwog5z93/files/a/c/d/dataset_acdbe52d-d41b-4afa-bbb8-821138ed527b.dat' 'forward_input.bam' && ln -s '/tmp/tmpdwog5z93/files/b/1/2/dataset_b125d42c-4cac-4761-97b3-a8b05b851af9.dat' 'reverse_input.bam' && bellerophon --forward forward_input.bam --reverse reverse_input.bam --quality 20 --output 'merged_out.bam' --threads ${GALAXY_SLOTS:-1} && samtools sort --no-PG -O BAM -o '/tmp/tmpdwog5z93/job_working_directory/000/28/outputs/dataset_fcb227d6-71de-4bc2-ade9-7383eb6f745c.dat' -@ ${GALAXY_SLOTS:-1} merged_out.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 32: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpdwog5z93/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpdwog5z93/files/3/4/d/dataset_34deabee-d8ac-48f9-8f94-e42e0291ab31.dat' 'c5,c6' T '/tmp/tmpdwog5z93/job_working_directory/000/36/outputs/dataset_19a1d6a2-fed4-4f37-9cce-ea18a20bdac2.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 33: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpdwog5z93/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpdwog5z93/files/3/4/d/dataset_34deabee-d8ac-48f9-8f94-e42e0291ab31.dat' 'c4,c7' T '/tmp/tmpdwog5z93/job_working_directory/000/37/outputs/dataset_84cabf7f-a0c4-4d85-a37f-cc579ff4957e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 34: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmpdwog5z93/files/f/c/b/dataset_fcb227d6-71de-4bc2-ade9-7383eb6f745c.dat' | PretextMap -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 83 sequences, sorted by length, descending. Filtering by minimum mapping quality 10

                                                                                
[PretextMap status] :: 10.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 10.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 15.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 20.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 25.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 30.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 35.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 40.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 45.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 50.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 55.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 60.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 65.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 70.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 75.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 80.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 85.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 90.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 95.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 100.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 105.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 109.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 114.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 119.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 124.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 130.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 135.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 139.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 144.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 149.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 154.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 159.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 164.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 169.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 174.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 179.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 184.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 190.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 195.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 199.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 204.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 209.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 214.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 219.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 224.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 229.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 234.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 239.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 245.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 250.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 255.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 260.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 265.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 270.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 275.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 280.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 285.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 290.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 294.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 300.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 305.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 310.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 314.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 640.0 k reads processed, 320.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 650.0 k reads processed, 325.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 660.0 k reads processed, 330.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 670.0 k reads processed, 335.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 680.0 k reads processed, 340.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 690.0 k reads processed, 345.0 k read-pairs mapped
[PretextMap status] :: Creating MipMaps...
[PretextMap status] :: Equalising contrast...
[PretextMap status] :: Compressing textures...

[PretextMap status] ::   1/528 (0.19%) texture blocks written to disk
[PretextMap status] ::   2/528 (0.38%) texture blocks written to disk
[PretextMap status] ::   3/528 (0.57%) texture blocks written to disk
[PretextMap status] ::   4/528 (0.76%) texture blocks written to disk
[PretextMap status] ::   5/528 (0.95%) texture blocks written to disk
[PretextMap status] ::   6/528 (1.14%) texture blocks written to disk
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[PretextMap status] ::   9/528 (1.70%) texture blocks written to disk
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..
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[PretextMap status] :: 489/528 (92.61%) texture blocks written to disk
[PretextMap status] :: 490/528 (92.80%) texture blocks written to disk
[PretextMap status] :: 491/528 (92.99%) texture blocks written to disk
[PretextMap status] :: 492/528 (93.18%) texture blocks written to disk
[PretextMap status] :: 493/528 (93.37%) texture blocks written to disk
[PretextMap status] :: 494/528 (93.56%) texture blocks written to disk
[PretextMap status] :: 495/528 (93.75%) texture blocks written to disk
[PretextMap status] :: 496/528 (93.94%) texture blocks written to disk
[PretextMap status] :: 497/528 (94.13%) texture blocks written to disk
[PretextMap status] :: 498/528 (94.32%) texture blocks written to disk
[PretextMap status] :: 499/528 (94.51%) texture blocks written to disk
[PretextMap status] :: 500/528 (94.70%) texture blocks written to disk
[PretextMap status] :: 501/528 (94.89%) texture blocks written to disk
[PretextMap status] :: 502/528 (95.08%) texture blocks written to disk
[PretextMap status] :: 503/528 (95.27%) texture blocks written to disk
[PretextMap status] :: 504/528 (95.45%) texture blocks written to disk
[PretextMap status] :: 505/528 (95.64%) texture blocks written to disk
[PretextMap status] :: 506/528 (95.83%) texture blocks written to disk
[PretextMap status] :: 507/528 (96.02%) texture blocks written to disk
[PretextMap status] :: 508/528 (96.21%) texture blocks written to disk
[PretextMap status] :: 509/528 (96.40%) texture blocks written to disk
[PretextMap status] :: 510/528 (96.59%) texture blocks written to disk
[PretextMap status] :: 511/528 (96.78%) texture blocks written to disk
[PretextMap status] :: 512/528 (96.97%) texture blocks written to disk
[PretextMap status] :: 513/528 (97.16%) texture blocks written to disk
[PretextMap status] :: 514/528 (97.35%) texture blocks written to disk
[PretextMap status] :: 515/528 (97.54%) texture blocks written to disk
[PretextMap status] :: 516/528 (97.73%) texture blocks written to disk
[PretextMap status] :: 517/528 (97.92%) texture blocks written to disk
[PretextMap status] :: 518/528 (98.11%) texture blocks written to disk
[PretextMap status] :: 519/528 (98.30%) texture blocks written to disk
[PretextMap status] :: 520/528 (98.48%) texture blocks written to disk
[PretextMap status] :: 521/528 (98.67%) texture blocks written to disk
[PretextMap status] :: 522/528 (98.86%) texture blocks written to disk
[PretextMap status] :: 523/528 (99.05%) texture blocks written to disk
[PretextMap status] :: 524/528 (99.24%) texture blocks written to disk
[PretextMap status] :: 525/528 (99.43%) texture blocks written to disk
[PretextMap status] :: 526/528 (99.62%) texture blocks written to disk
[PretextMap status] :: 527/528 (99.81%) texture blocks written to disk
[PretextMap status] :: 528/528 (100.00%) texture blocks written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpdwog5z93/files/f/c/b/dataset_fcb227d6-71de-4bc2-ade9-7383eb6f745c.dat' ./input.bam &&  bedtools bamtobed -bed12   -i ./input.bam > '/tmp/tmpdwog5z93/job_working_directory/000/30/outputs/dataset_53ab58bb-9ae4-44d4-bd16-e76c6f7064b9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ed_score	`false`
option	`"-bed12"`
split	`false`
tag	`""`

Step 36: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpdwog5z93/job_working_directory/000/38/configs/tmpa_n3us3l' && Rscript '/tmp/tmpdwog5z93/job_working_directory/000/38/configs/tmpa_n3us3l'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpdwog5z93/files/1/9/a/dataset_19a1d6a2-fed4-4f37-9cce-ea18a20bdac2.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpdwog5z93/job_working_directory/000/38/outputs/dataset_0a6e8e8c-a6be-4d52-b2ef-b57b0c65bf1e.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"x"`
xplot	`"1"`
ylab	`"Nx (Mb)"`
yplot	`"2"`

Step 37: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpdwog5z93/job_working_directory/000/39/configs/tmpcazxthif' && Rscript '/tmp/tmpdwog5z93/job_working_directory/000/39/configs/tmpcazxthif'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpdwog5z93/files/8/4/c/dataset_84cabf7f-a0c4-4d85-a37f-cc579ff4957e.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpdwog5z93/job_working_directory/000/39/outputs/dataset_e2f0f505-fe6a-45bd-a78c-e07925157b27.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"1"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"2"`

Step 38: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmpdwog5z93/files/b/0/1/dataset_b014b491-8823-45b4-8330-38cdcac96d0d.dat -f png -r 1000 -c 5 --sequences '=full' --minTexels 64 --gridSize 1 --gridColour black '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmpdwog5z93/files/b/0/1/dataset_b014b491-8823-45b4-8330-38cdcac96d0d.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 1000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 1 pixel
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 0, "gridcolor": "black", "gridsize": "1", "showGrid": "yes"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 39: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

( LC_ALL=C  sort   --stable -t '	'  -k '4,4'  ) < '/tmp/tmpdwog5z93/files/5/3/a/dataset_53ab58bb-9ae4-44d4-bd16-e76c6f7064b9.dat' > '/tmp/tmpdwog5z93/job_working_directory/000/32/outputs/dataset_81d174d4-8a45-4a8c-b253-dbf661b4e314.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
chromInfo	`"/tmp/tmpdwog5z93/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`"0"`
ignore_case	`false`
sortkeys	`[{"__index__": 0, "column": "4", "order": "", "style": ""}]`
unique	`false`

Step 40: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"6f6d0e7c89e611efb6216045bd0674c9"`
input	`{"values": [{"id": 5, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 5: Lineage:
- step_state: scheduled
Step 6: HiC Forward reads:
- step_state: scheduled
Step 7: HiC reverse reads:
- step_state: scheduled
Step 8: Restriction enzymes:
- step_state: scheduled
Step 9: Estimated genome size - Parameter File:
- step_state: scheduled
Step 10: SAK input file:
- step_state: scheduled

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - d8262246089cdb14
- history_state
  - error
- invocation_id
  - d8262246089cdb14
- invocation_state
  - scheduled
- workflow_id
  - 1c404bd5e0a738b8

github-actions · 2024-10-23T20:39:31Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '43' (Trim Hi-C Data?) is not optional and no input provided.","err_code":0}

github-actions · 2024-10-23T20:39:48Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '38' (Collection Hi-C forward reads) is not optional and no input provided.","err_code":0}

github-actions · 2024-10-23T20:40:00Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '43' (Trim Hi-C Data?) is not optional and no input provided.","err_code":0}

github-actions · 2024-10-23T20:47:55Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Final state of invocation 7a6de5a75368a785 is [failed]

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred.

Steps

Step 1: Input GFA:
- step_state: scheduled
Step 2: Haplotype:
- step_state: scheduled
Step 11: SAK input file:
- step_state: scheduled

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"95a14c02917f11efa92069478e5305ab"`
chromInfo	`"/tmp/tmpleha1bua/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "$&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "hap1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 13: Unlabelled step:
- step_state: new
Step 3: Sequence graph:
- step_state: scheduled
Step 4: Trim Hi-C Data?:
- step_state: scheduled
Step 5: Collection Hi-C forward reads:
- step_state: scheduled
Step 6: Collection Hi-C reverse reads:
- step_state: scheduled
Step 7: Database for Busco Lineage:
- step_state: scheduled
Step 8: Lineage:
- step_state: scheduled
Step 9: Restriction enzymes:
- step_state: scheduled
Step 10: Estimated genome size - Parameter File:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation 7a6de5a75368a785 is [failed]
- history_id
  - 7a6de5a75368a785
- history_state
  - ok
- invocation_id
  - 7a6de5a75368a785
- invocation_state
  - failed
- messages
  - [{'details': None, 'reason': 'unexpected_failure', 'workflow_step_id': None}]
- workflow_id
  - 3f3562e84e60f744

github-actions · 2024-10-23T21:09:45Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Final state of invocation b2167f49b522f99b is [failed]

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred.

Steps

Step 1: Input GFA:
- step_state: scheduled
Step 2: Haplotype:
- step_state: scheduled
Step 11: SAK input file:
- step_state: scheduled

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"335c4ad0918211ef9e2959afaf2d53f1"`
chromInfo	`"/tmp/tmpu6h1n4fy/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "$&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "hap1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 13: Unlabelled step:
- step_state: new
Step 3: Sequence graph:
- step_state: scheduled
Step 4: Trim Hi-C Data?:
- step_state: scheduled
Step 5: Collection Hi-C forward reads:
- step_state: scheduled
Step 6: Collection Hi-C reverse reads:
- step_state: scheduled
Step 7: Database for Busco Lineage:
- step_state: scheduled
Step 8: Lineage:
- step_state: scheduled
Step 9: Restriction enzymes:
- step_state: scheduled
Step 10: Estimated genome size - Parameter File:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation b2167f49b522f99b is [failed]
- history_id
  - b2167f49b522f99b
- history_state
  - ok
- invocation_id
  - b2167f49b522f99b
- invocation_state
  - failed
- messages
  - [{'details': None, 'reason': 'unexpected_failure', 'workflow_step_id': None}]
- workflow_id
  - 1e9087b744dcac84

github-actions · 2024-10-23T21:09:56Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Final state of invocation 629edda611b0ae8e is [failed]

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred.

Steps

Step 1: Input GFA:
- step_state: scheduled
Step 2: Haplotype:
- step_state: scheduled
Step 11: SAK input file:
- step_state: scheduled

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"60cf31ee918211ef88501d3bd3a74eb0"`
chromInfo	`"/tmp/tmp1z3yo_ri/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "$&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "hap1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 13: Unlabelled step:
- step_state: new
Step 3: Sequence graph:
- step_state: scheduled
Step 4: Trim Hi-C Data?:
- step_state: scheduled
Step 5: Collection Hi-C forward reads:
- step_state: scheduled
Step 6: Collection Hi-C reverse reads:
- step_state: scheduled
Step 7: Database for Busco Lineage:
- step_state: scheduled
Step 8: Lineage:
- step_state: scheduled
Step 9: Restriction enzymes:
- step_state: scheduled
Step 10: Estimated genome size - Parameter File:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation 629edda611b0ae8e is [failed]
- history_id
  - 629edda611b0ae8e
- history_state
  - ok
- invocation_id
  - 629edda611b0ae8e
- invocation_state
  - failed
- messages
  - [{'details': None, 'reason': 'unexpected_failure', 'workflow_step_id': None}]
- workflow_id
  - 15c6c7ef56133f1b

github-actions · 2024-10-24T14:29:36Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Scaffolding-HiC-VGP8.ga_0

Problems:

Output with path /tmp/tmppl1mx628/Reconciliated Scaffolds gfa__70d94c31-c775-42b5-8915-c5a59700a126 different than expected
Expected 169+-0 lines in the output found 168

Output with path /tmp/tmpj4lvq8l4/gfastats on data 32 edited sequences__ad372717-5464-4178-b45e-609785ffda51 different than expected
Expected 168+-0 lines in the output found 166

Output with path /tmp/tmp0c6_2y4y/gfastats on data 32 stats__f115811c-d28f-4341-a1c7-2b33d8642a43 different than expected
Expected line '# scaffolds	84' in output ('Expected genome size	2,288,021
# scaffolds	83
Total scaffold length	1,971,489
Average scaffold length	23,752.88
Scaffold N50	20,934
Scaffold auN	34,029.81
Scaffold L50	30
Scaffold NG50	20,241
Scaffold auNG	29,322.02
Scaffold LG50	37
Largest scaffold	132,632
Smallest scaffold	11,828
# contigs	83
Total contig length	1,971,489
Average contig length	23,752.88
Contig N50	20,934
Contig auN	34,029.81
Contig L50	30
Contig NG50	20,241
Contig auNG	29,322.02
Contig LG50	37
Largest contig	132,632
Smallest contig	11,828
# gaps in scaffolds	0
Total gap length in scaffolds	0
Average gap length in scaffolds	0.00
Gap N50 in scaffolds	0
Gap auN in scaffolds	0.00
Gap L50 in scaffolds	0
Largest gap in scaffolds	0
Smallest gap in scaffolds	0
Base composition (A:C:G:T)	603,206:382,062:383,274:602,947
GC content %	38.82
# soft-masked bases	0
# segments	84
Total segment length	1,982,895
Average segment length	23,605.89
# gaps	0
# paths	83
Scaffold N10	93,719
Scaffold N20	38,264
Scaffold N30	26,760
Scaffold N40	24,008
Scaffold N50	20,934
Scaffold N60	20,055
Scaffold N70	19,466
Scaffold N80	18,496
Scaffold N90	17,261
Scaffold N100	11,828
Scaffold L10	2
Scaffold L20	7
Scaffold L30	13
Scaffold L40	21
Scaffold L50	30
Scaffold L60	39
Scaffold L70	49
Scaffold L80	60
Scaffold L90	71
Scaffold L100	83
Scaffold NG10	43,860
Scaffold NG20	33,978
Scaffold NG30	24,984
Scaffold NG40	22,011
Scaffold NG50	20,241
Scaffold NG60	19,466
Scaffold NG70	18,480
Scaffold NG80	16,794
Scaffold NG90	0
Scaffold NG100	0
Scaffold LG10	3
Scaffold LG20	8
Scaffold LG30	17
Scaffold LG40	26
Scaffold LG50	37
Scaffold LG60	49
Scaffold LG70	61
Scaffold LG80	74
Scaffold LG90	0
Scaffold LG100	0
Contig N10	93,719
Contig N20	38,264
Contig N30	26,760
Contig N40	24,008
Contig N50	20,934
Contig N60	20,055
Contig N70	19,466
Contig N80	18,496
Contig N90	17,261
Contig N100	11,828
Contig L10	2
Contig L20	7
Contig L30	13
Contig L40	21
Contig L50	30
Contig L60	39
Contig L70	49
Contig L80	60
Contig L90	71
Contig L100	83
Contig NG10	43,860
Contig NG20	33,978
Contig NG30	24,984
Contig NG40	22,011
Contig NG50	20,241
Contig NG60	19,466
Contig NG70	18,480
Contig NG80	16,794
Contig NG90	0
Contig NG100	0
Contig LG10	3
Contig LG20	8
Contig LG30	17
Contig LG40	26
Contig LG50	37
Contig LG60	49
Contig LG70	61
Contig LG80	74
Contig LG90	0
Contig LG100	0
Gap N10	0
Gap N20	0
Gap N30	0
Gap N40	0
Gap N50	0
Gap N60	0
Gap N70	0
Gap N80	0
Gap N90	0
Gap N100	0
Gap L10	0
Gap L20	0
Gap L30	0
Gap L40	0
Gap L50	0
Gap L60	0
Gap L70	0
Gap L80	0
Gap L90	0
Gap L100	0
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Input GFA:
- step_state: scheduled
Step 2: Haplotype:
- step_state: scheduled
Step 11: SAK input file:
- step_state: scheduled

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "$&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "hap1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 13: __SORTLIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
input	`{"values": [{"id": 1, "src": "hdca"}]}`
sort_type	`{"__current_case__": 0, "sort_type": "alpha"}`

Step 14: __SORTLIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
input	`{"values": [{"id": 2, "src": "hdca"}]}`
sort_type	`{"__current_case__": 0, "sort_type": "alpha"}`

Step 15: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpos9o7_en/files/0/7/d/dataset_07d5671b-b713-4ed7-9ebf-d2d6301079e5.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 84
Total scaffold length: 1982895
Average scaffold length: 23605.89
Scaffold N50: 20934
Scaffold auN: 33899.67
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 84
Total contig length: 1982895
Average contig length: 23605.89
Contig N50: 20934
Contig auN: 33899.67
Contig L50: 30
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 606458:383991:386001:606445
GC content %: 38.83
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 84
# edges: 4
Average degree: 0.05
# connected components: 1
Largest connected component length: 94650
# dead ends: 165
# disconnected components: 81
Total length disconnected components: 1888245
# separated components: 82
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 17: Hi-C Forward reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

(   cat "/tmp/tmpos9o7_en/files/f/7/6/dataset_f76b6060-5faa-4bc9-8e37-d879a4782fbc.dat" ;   ) > /tmp/tmpos9o7_en/job_working_directory/000/10/outputs/dataset_cdbe3f1a-1b48-440c-a266-637240ba8be4.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 18: Hi-C Reverse reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

(   cat "/tmp/tmpos9o7_en/files/8/e/0/dataset_8e0dedcc-9f4d-486d-95e3-f9150937c279.dat" ;   ) > /tmp/tmpos9o7_en/job_working_directory/000/11/outputs/dataset_552236de-d8a1-484f-94fe-b6beafe1dc85.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 19: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	`{"__current_case__": 1, "input_1": {"values": [{"id": 10, "src": "hda"}]}, "input_2": {"values": [{"id": 11, "src": "hda"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired"}`
other_trimming_options	`{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`None`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 20: Pick forward reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 12, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 10, "src": "hda"}]}}]}}`

Step 3: Sequence graph:
- step_state: scheduled

Step 21: Pick reverse reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 13, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 11, "src": "hda"}]}}]}}`

Step 22: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpos9o7_en/files/e/5/6/dataset_e5650dd2-4fd2-4bc5-a914-c9fa4c978db9.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpos9o7_en/files/c/d/b/dataset_cdbe3f1a-1b48-440c-a266-637240ba8be4.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpos9o7_en/job_working_directory/000/15/outputs/dataset_d49fbb22-0951-4180-b343-3fb52e32af29.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 145145399
ref seq len = 3965790
binary seq ticks = 75199467
build suffix-array ticks = 682613512
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 199344756
Total time taken: 0.4646
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 3041008
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000037, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000037 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000053, nseq: 100108
	[0000][ M::kt_pipeline] read 100108 sequences (10000053 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 5.295 CPU sec, 5.315 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000072, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000072 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100108 reads in 5.306 CPU sec, 5.390 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000203, nseq: 100132
	[0000][ M::kt_pipeline] read 100132 sequences (10000203 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 5.443 CPU sec, 5.535 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000073, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000073 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100132 reads in 5.418 CPU sec, 5.514 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000141, nseq: 100166
	[0000][ M::kt_pipeline] read 100166 sequences (10000141 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 5.240 CPU sec, 5.340 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000104, nseq: 118598
	[0000][ M::kt_pipeline] read 118598 sequences (10000104 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100166 reads in 5.311 CPU sec, 5.414 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000109, nseq: 151884
	[0000][ M::kt_pipeline] read 151884 sequences (10000109 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118598 reads in 5.284 CPU sec, 5.372 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000126, nseq: 151908
	[0000][ M::kt_pipeline] read 151908 sequences (10000126 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151884 reads in 4.974 CPU sec, 5.067 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151908 reads in 4.986 CPU sec, 5.096 real sec
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000007, nseq: 151868
	[0000][ M::kt_pipeline] read 151868 sequences (10000007 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 5.083 CPU sec, 5.185 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000077, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000077 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151868 reads in 4.889 CPU sec, 4.993 real sec
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000024, nseq: 127818
	[0000][ M::kt_pipeline] read 127818 sequences (10000024 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 4.975 CPU sec, 5.079 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000071, nseq: 98956
	[0000][ M::kt_pipeline] read 98956 sequences (10000071 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127818 reads in 6.685 CPU sec, 6.799 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000004, nseq: 145156
	[0000][ M::kt_pipeline] read 145156 sequences (10000004 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98956 reads in 8.788 CPU sec, 8.884 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3496096, nseq: 53016
	[0000][ M::kt_pipeline] read 53016 sequences (3496096 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145156 reads in 7.540 CPU sec, 7.628 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 53016 reads in 2.671 CPU sec, 2.785 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.604259 MHz
Runtime profile:

	Time taken for main_mem function: 89.62 sec

	IO times (sec) :
	Reading IO time (reads) avg: 4.89, (4.89, 4.89)
	Writing IO time (SAM) avg: 3.90, (3.90, 3.90)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.00, (0.00, 0.00)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 89.61
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 89.39, (89.39, 89.39)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 8.16, (8.16, 8.16)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 81.23, (81.23, 81.23)
		SMEM compute avg: 26.52, (26.52, 26.52)
		SAL compute avg: 17.20, (17.20, 17.20)
				MEM_SA avg: 8.92, (8.92, 8.92)

		BSW time, avg: 32.35, (32.35, 32.35)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[3041008] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 14, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpos9o7_en/files/e/5/6/dataset_e5650dd2-4fd2-4bc5-a914-c9fa4c978db9.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpos9o7_en/files/5/5/2/dataset_552236de-d8a1-484f-94fe-b6beafe1dc85.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpos9o7_en/job_working_directory/000/16/outputs/dataset_6a20c8e6-fae6-42d5-959f-c93ca09ed0fa.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 129688006
ref seq len = 3965790
binary seq ticks = 74505063
build suffix-array ticks = 701358389
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 219532225
Total time taken: 0.4714
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 3041008
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000036, nseq: 100212
	[0000][ M::kt_pipeline] read 100212 sequences (10000036 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000140, nseq: 100074
	[0000][ M::kt_pipeline] read 100074 sequences (10000140 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100212 reads in 5.363 CPU sec, 5.374 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000066, nseq: 100106
	[0000][ M::kt_pipeline] read 100106 sequences (10000066 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100074 reads in 5.429 CPU sec, 5.506 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000070, nseq: 100180
	[0000][ M::kt_pipeline] read 100180 sequences (10000070 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100106 reads in 5.471 CPU sec, 5.557 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000000, nseq: 100202
	[0000][ M::kt_pipeline] read 100202 sequences (10000000 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100180 reads in 5.385 CPU sec, 5.462 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000132, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000132 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100202 reads in 5.351 CPU sec, 5.443 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 118588
	[0000][ M::kt_pipeline] read 118588 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 5.294 CPU sec, 5.382 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000125, nseq: 151900
	[0000][ M::kt_pipeline] read 151900 sequences (10000125 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118588 reads in 5.187 CPU sec, 5.268 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000005, nseq: 151874
	[0000][ M::kt_pipeline] read 151874 sequences (10000005 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151900 reads in 4.843 CPU sec, 4.950 real sec
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151904
	[0000][ M::kt_pipeline] read 151904 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151874 reads in 4.763 CPU sec, 4.872 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151896
	[0000][ M::kt_pipeline] read 151896 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151904 reads in 4.901 CPU sec, 5.013 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000130, nseq: 151906
	[0000][ M::kt_pipeline] read 151906 sequences (10000130 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151896 reads in 4.993 CPU sec, 5.106 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 127808
	[0000][ M::kt_pipeline] read 127808 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151906 reads in 4.912 CPU sec, 5.024 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000028, nseq: 98948
	[0000][ M::kt_pipeline] read 98948 sequences (10000028 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127808 reads in 6.519 CPU sec, 6.639 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000026, nseq: 145218
	[0000][ M::kt_pipeline] read 145218 sequences (10000026 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98948 reads in 8.477 CPU sec, 8.588 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3489223, nseq: 52906
	[0000][ M::kt_pipeline] read 52906 sequences (3489223 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145218 reads in 7.348 CPU sec, 7.451 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 52906 reads in 2.680 CPU sec, 2.779 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.717552 MHz
Runtime profile:

	Time taken for main_mem function: 88.67 sec

	IO times (sec) :
	Reading IO time (reads) avg: 4.84, (4.84, 4.84)
	Writing IO time (SAM) avg: 3.78, (3.78, 3.78)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.00, (0.00, 0.00)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 88.67
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 88.41, (88.41, 88.41)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 8.32, (8.32, 8.32)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 80.08, (80.08, 80.08)
		SMEM compute avg: 26.61, (26.61, 26.61)
		SAL compute avg: 16.76, (16.76, 16.76)
				MEM_SA avg: 8.33, (8.33, 8.33)

		BSW time, avg: 32.00, (32.00, 32.00)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[3041008] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 15, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpos9o7_en/files/d/4/9/dataset_d49fbb22-0951-4180-b343-3fb52e32af29.dat' 'forward_input.bam' && ln -s '/tmp/tmpos9o7_en/files/6/a/2/dataset_6a20c8e6-fae6-42d5-959f-c93ca09ed0fa.dat' 'reverse_input.bam' && bellerophon --forward forward_input.bam --reverse reverse_input.bam --quality 20 --output 'merged_out.bam' --threads ${GALAXY_SLOTS:-1} && samtools sort --no-PG -O BAM -o '/tmp/tmpos9o7_en/job_working_directory/000/17/outputs/dataset_e5b981d3-6794-4c65-b75b-414c7255b014.dat' -@ ${GALAXY_SLOTS:-1} merged_out.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmpos9o7_en/files/e/5/b/dataset_e5b981d3-6794-4c65-b75b-414c7255b014.dat' | PretextMap -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 84 sequences, sorted by length, descending. Filtering by minimum mapping quality 10

                                                                                
[PretextMap status] :: 10.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 10.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 15.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 20.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 25.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 30.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 35.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 40.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 45.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 50.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 55.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 60.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 65.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 70.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 75.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 80.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 85.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 90.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 95.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 100.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 104.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 109.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 114.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 119.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 124.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 129.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 134.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 139.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 145.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 150.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 154.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 159.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 165.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 170.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 175.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 180.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 185.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 190.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 195.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 200.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 205.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 210.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 215.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 220.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 225.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 230.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 235.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 240.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 245.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 250.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 255.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 260.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 265.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 270.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 275.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 280.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 285.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 290.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 295.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 300.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 305.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 310.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 315.0 k read-pairs mapped
                                                                                
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[PretextMap status] :: 690.0 k reads processed, 345.0 k read-pairs mapped
[PretextMap status] :: Creating MipMaps...
[PretextMap status] :: Equalising contrast...
[PretextMap status] :: Compressing textures...

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Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpos9o7_en/files/e/5/6/dataset_e5650dd2-4fd2-4bc5-a914-c9fa4c978db9.dat' input.fasta && ln -s '/tmp/tmpos9o7_en/files/e/5/b/dataset_e5b981d3-6794-4c65-b75b-414c7255b014.dat' input.bam && samtools faidx input.fasta && mkdir initial_break agp_out agp_break final_outs && yahs --no-mem-check input.fasta input.bam -e 'GATC,GANTC,CTNAG,TTAA' --no-contig-ec  -o yahs_out 2> output.log && ls -lah && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/yahs/ff4031bfaa22/yahs/move_files.py' && ls -lah ./*

Exit Code:

```
0
```

Standard Output:

total 8M     
drwxr-xr-x    6 1001     127         4.0K Oct 24 13:54 .
drwxr-xr-x   12 1001     127         4.0K Oct 24 13:54 ..
drwxr-xr-x    2 1001     127         4.0K Oct 24 13:54 agp_break
drwxr-xr-x    2 1001     127         4.0K Oct 24 13:54 agp_out
drwxr-xr-x    2 1001     127         4.0K Oct 24 13:54 final_outs
drwxr-xr-x    2 1001     127         4.0K Oct 24 13:54 initial_break
lrwxrwxrwx    1 1001     127           77 Oct 24 13:54 input.bam -> /tmp/tmpos9o7_en/files/e/5/b/dataset_e5b981d3-6794-4c65-b75b-414c7255b014.dat
lrwxrwxrwx    1 1001     127           77 Oct 24 13:54 input.fasta -> /tmp/tmpos9o7_en/files/e/5/6/dataset_e5650dd2-4fd2-4bc5-a914-c9fa4c978db9.dat
-rw-r--r--    1 1001     127         3.5K Oct 24 13:54 input.fasta.fai
-rw-r--r--    1 1001     127         5.1K Oct 24 13:54 output.log
-rw-r--r--    1 1001     127         5.6M Oct 24 13:54 yahs_out.bin
-rw-r--r--    1 1001     127         4.2K Oct 24 13:54 yahs_out_no_break.agp
-rw-r--r--    1 1001     127         4.2K Oct 24 13:54 yahs_out_scaffolds_final.agp
-rw-r--r--    1 1001     127         1.9M Oct 24 13:54 yahs_out_scaffolds_final.fa
lrwxrwxrwx    1 1001     127           77 Oct 24 13:54 ./input.bam -> /tmp/tmpos9o7_en/files/e/5/b/dataset_e5b981d3-6794-4c65-b75b-414c7255b014.dat
lrwxrwxrwx    1 1001     127           77 Oct 24 13:54 ./input.fasta -> /tmp/tmpos9o7_en/files/e/5/6/dataset_e5650dd2-4fd2-4bc5-a914-c9fa4c978db9.dat
-rw-r--r--    1 1001     127         3.5K Oct 24 13:54 ./input.fasta.fai
-rw-r--r--    1 1001     127         5.1K Oct 24 13:54 ./output.log
-rw-r--r--    1 1001     127         5.6M Oct 24 13:54 ./yahs_out.bin

./agp_break:
total 16K    
drwxr-xr-x    2 1001     127         4.0K Oct 24 13:54 .
drwxr-xr-x    6 1001     127         4.0K Oct 24 13:54 ..
-rw-r--r--    1 1001     127         4.2K Oct 24 13:54 yahs_out_no_break.agp

./agp_out:
total 8K     
drwxr-xr-x    2 1001     127         4.0K Oct 24 13:54 .
drwxr-xr-x    6 1001     127         4.0K Oct 24 13:54 ..

./final_outs:
total 2M     
drwxr-xr-x    2 1001     127         4.0K Oct 24 13:54 .
drwxr-xr-x    6 1001     127         4.0K Oct 24 13:54 ..
-rw-r--r--    1 1001     127         4.2K Oct 24 13:54 yahs_out_scaffolds_final.agp
-rw-r--r--    1 1001     127         1.9M Oct 24 13:54 yahs_out_scaffolds_final.fa

./initial_break:
total 8K     
drwxr-xr-x    2 1001     127         4.0K Oct 24 13:54 .
drwxr-xr-x    6 1001     127         4.0K Oct 24 13:54 ..

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function	`{"__current_case__": 0, "agp": null, "bfile": {"values": [{"id": 18, "src": "hda"}]}, "enzyme_conditional": {"__current_case__": 1, "enzyme_options": "preconfigured", "preconfigured_enzymes": "arima2"}, "fasta": {"values": [{"id": 9, "src": "hda"}]}, "function_select": "yahs", "length": null, "no_contig_ec": true, "no_scaffold_ec": false, "quality": null, "res": ""}`
log_out	`true`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmpos9o7_en/files/a/c/2/dataset_ac2cdc22-d1eb-4655-99a5-da4b82e02579.dat -f png -r 1000 -c 5 --sequences '=full' --minTexels 64 --gridSize 0 '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmpos9o7_en/files/a/c/2/dataset_ac2cdc22-d1eb-4655-99a5-da4b82e02579.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 1000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 0 pixels
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 1, "showGrid": "no"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmpos9o7_en/job_working_directory/000/21/outputs/dataset_ad5d7ba2-c08d-4eb4-b27b-7c5c8ad7774f.dat' -g  -w  -r 'scaffold_[0-9]*' '$&.hap1' '/tmp/tmpos9o7_en/files/6/f/8/dataset_6f83a924-2922-4918-8d8b-b9f7d8c92b44.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "scaffold_[0-9]*", "global": true, "is_regex": true, "replace_pattern": "$&.hap1", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": true}]`

Step 29: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
input	`{"values": [{"id": 8, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpos9o7_en/files/e/5/6/dataset_e5650dd2-4fd2-4bc5-a914-c9fa4c978db9.dat' --agp-to-path /tmp/tmpos9o7_en/files/a/d/5/dataset_ad5d7ba2-c08d-4eb4-b27b-7c5c8ad7774f.dat  -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 83
Total scaffold length: 1971489
Average scaffold length: 23752.88
Scaffold N50: 20934
Scaffold auN: 34029.81
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11828
# contigs: 83
Total contig length: 1971489
Average contig length: 23752.88
Contig N50: 20934
Contig auN: 34029.81
Contig L50: 30
Largest contig: 132632
Smallest contig: 11828
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 603206:382062:383274:602947
GC content %: 38.82
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 83

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 2, "agp_to_path": {"values": [{"id": 23, "src": "hda"}]}, "discover_paths": false, "selector": "scaffolding"}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 4: Trim Hi-C Data?:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpos9o7_en/files/7/0/d/dataset_70d94c31-c775-42b5-8915-c5a59700a126.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 83
Total scaffold length: 1971489
Average scaffold length: 23752.88
Scaffold N50: 20934
Scaffold auN: 34029.81
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11828
# contigs: 83
Total contig length: 1971489
Average contig length: 23752.88
Contig N50: 20934
Contig auN: 34029.81
Contig L50: 30
Largest contig: 132632
Smallest contig: 11828
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 603206:382062:383274:602947
GC content %: 38.82
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 83

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpos9o7_en/files/7/0/d/dataset_70d94c31-c775-42b5-8915-c5a59700a126.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmpos9o7_en/job_working_directory/000/24/outputs/dataset_f115811c-d28f-4341-a1c7-2b33d8642a43.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 33: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpos9o7_en/files/7/0/d/dataset_70d94c31-c775-42b5-8915-c5a59700a126.dat' --out-size s   --tabular > '/tmp/tmpos9o7_en/job_working_directory/000/25/outputs/dataset_9ab9a254-e4f8-49d8-b02c-e0fbda6c157c.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "s", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 34: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpos9o7_en/files/a/d/3/dataset_ad372717-5464-4178-b45e-609785ffda51.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpos9o7_en/files/c/d/b/dataset_cdbe3f1a-1b48-440c-a266-637240ba8be4.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpos9o7_en/job_working_directory/000/26/outputs/dataset_61bd5ccf-2a44-4829-9641-b34891f50007.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 258732643
ref seq len = 3942978
binary seq ticks = 139034879
build suffix-array ticks = 1120661825
pos: 492873, ref_seq_len__: 492872
build fm-index ticks = 278911242
Total time taken: 0.7755
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3942979
* sentinel-index: 3258568
* Count:
0,	1
1,	1206154
2,	1971490
3,	2736826
4,	3942979

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3942978 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000037, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000037 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000053, nseq: 100108
	[0000][ M::kt_pipeline] read 100108 sequences (10000053 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 6.882 CPU sec, 8.399 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000072, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000072 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100108 reads in 7.193 CPU sec, 8.542 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000203, nseq: 100132
	[0000][ M::kt_pipeline] read 100132 sequences (10000203 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 7.207 CPU sec, 8.310 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000073, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000073 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100132 reads in 7.131 CPU sec, 7.833 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000141, nseq: 100166
	[0000][ M::kt_pipeline] read 100166 sequences (10000141 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 6.967 CPU sec, 8.105 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000104, nseq: 118598
	[0000][ M::kt_pipeline] read 118598 sequences (10000104 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100166 reads in 6.986 CPU sec, 7.957 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000109, nseq: 151884
	[0000][ M::kt_pipeline] read 151884 sequences (10000109 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118598 reads in 6.950 CPU sec, 8.311 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000126, nseq: 151908
	[0000][ M::kt_pipeline] read 151908 sequences (10000126 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151884 reads in 6.525 CPU sec, 7.859 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151908 reads in 6.561 CPU sec, 7.388 real sec
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000007, nseq: 151868
	[0000][ M::kt_pipeline] read 151868 sequences (10000007 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 6.014 CPU sec, 7.348 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000077, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000077 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151868 reads in 6.139 CPU sec, 7.627 real sec
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000024, nseq: 127818
	[0000][ M::kt_pipeline] read 127818 sequences (10000024 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 5.939 CPU sec, 7.276 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000071, nseq: 98956
	[0000][ M::kt_pipeline] read 98956 sequences (10000071 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127818 reads in 8.263 CPU sec, 11.195 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000004, nseq: 145156
	[0000][ M::kt_pipeline] read 145156 sequences (10000004 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98956 reads in 10.924 CPU sec, 13.648 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3496096, nseq: 53016
	[0000][ M::kt_pipeline] read 53016 sequences (3496096 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145156 reads in 9.295 CPU sec, 10.857 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 53016 reads in 3.305 CPU sec, 3.907 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.619547 MHz
Runtime profile:

	Time taken for main_mem function: 134.97 sec

	IO times (sec) :
	Reading IO time (reads) avg: 6.48, (6.48, 6.48)
	Writing IO time (SAM) avg: 5.87, (5.87, 5.87)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 134.96
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 134.55, (134.55, 134.55)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 11.90, (11.90, 11.90)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 122.65, (122.65, 122.65)
		SMEM compute avg: 41.08, (41.08, 41.08)
		SAL compute avg: 23.68, (23.68, 23.68)
				MEM_SA avg: 12.22, (12.22, 12.22)

		BSW time, avg: 50.26, (50.26, 50.26)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3942978
count = 0, 1206153, 1971489, 2736825, 3942978
BWT[3258568] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61609

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 14, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 25, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpos9o7_en/files/a/d/3/dataset_ad372717-5464-4178-b45e-609785ffda51.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmpos9o7_en/files/5/5/2/dataset_552236de-d8a1-484f-94fe-b6beafe1dc85.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpos9o7_en/job_working_directory/000/27/outputs/dataset_3642ac5a-b369-4cf4-8909-54da5ba04d5e.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 152117075
ref seq len = 3942978
binary seq ticks = 88319756
build suffix-array ticks = 781052478
pos: 492873, ref_seq_len__: 492872
build fm-index ticks = 236437833
Total time taken: 0.5299
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3942979
* sentinel-index: 3258568
* Count:
0,	1
1,	1206154
2,	1971490
3,	2736826
4,	3942979

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3942978 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000036, nseq: 100212
	[0000][ M::kt_pipeline] read 100212 sequences (10000036 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000140, nseq: 100074
	[0000][ M::kt_pipeline] read 100074 sequences (10000140 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100212 reads in 6.784 CPU sec, 7.256 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000066, nseq: 100106
	[0000][ M::kt_pipeline] read 100106 sequences (10000066 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100074 reads in 6.877 CPU sec, 7.989 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000070, nseq: 100180
	[0000][ M::kt_pipeline] read 100180 sequences (10000070 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100106 reads in 7.298 CPU sec, 8.538 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000000, nseq: 100202
	[0000][ M::kt_pipeline] read 100202 sequences (10000000 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100180 reads in 6.997 CPU sec, 8.379 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000132, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000132 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100202 reads in 7.049 CPU sec, 7.903 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 118588
	[0000][ M::kt_pipeline] read 118588 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 7.044 CPU sec, 8.152 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000125, nseq: 151900
	[0000][ M::kt_pipeline] read 151900 sequences (10000125 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118588 reads in 6.874 CPU sec, 8.289 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000005, nseq: 151874
	[0000][ M::kt_pipeline] read 151874 sequences (10000005 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151900 reads in 6.352 CPU sec, 7.512 real sec
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151904
	[0000][ M::kt_pipeline] read 151904 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151874 reads in 6.672 CPU sec, 8.070 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151896
	[0000][ M::kt_pipeline] read 151896 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151904 reads in 6.536 CPU sec, 7.707 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000130, nseq: 151906
	[0000][ M::kt_pipeline] read 151906 sequences (10000130 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151896 reads in 6.238 CPU sec, 7.644 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 127808
	[0000][ M::kt_pipeline] read 127808 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151906 reads in 6.059 CPU sec, 7.859 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000028, nseq: 98948
	[0000][ M::kt_pipeline] read 98948 sequences (10000028 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127808 reads in 7.929 CPU sec, 9.851 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000026, nseq: 145218
	[0000][ M::kt_pipeline] read 145218 sequences (10000026 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98948 reads in 10.848 CPU sec, 14.140 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3489223, nseq: 52906
	[0000][ M::kt_pipeline] read 52906 sequences (3489223 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145218 reads in 9.234 CPU sec, 11.132 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 52906 reads in 3.194 CPU sec, 3.755 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.618302 MHz
Runtime profile:

	Time taken for main_mem function: 134.56 sec

	IO times (sec) :
	Reading IO time (reads) avg: 6.16, (6.16, 6.16)
	Writing IO time (SAM) avg: 6.05, (6.05, 6.05)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 134.55
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 134.17, (134.17, 134.17)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 12.18, (12.18, 12.18)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 121.98, (121.98, 121.98)
		SMEM compute avg: 40.25, (40.25, 40.25)
		SAL compute avg: 23.79, (23.79, 23.79)
				MEM_SA avg: 12.10, (12.10, 12.10)

		BSW time, avg: 50.26, (50.26, 50.26)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3942978
count = 0, 1206153, 1971489, 2736825, 3942978
BWT[3258568] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61609

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 15, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 25, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 36: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmpos9o7_en/files/a/d/3/dataset_ad372717-5464-4178-b45e-609785ffda51.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'vertebrata_odb10'  --metaeuk  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific

Exit Code:

```
0
```

Standard Error:

2024-10-24 14:17:50 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-10-24 13:57:05 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 10/24/2024 13:57:05 *****
2024-10-24 13:57:05 INFO:	Configuring BUSCO with local environment
2024-10-24 13:57:05 INFO:	Running genome mode
2024-10-24 13:57:07 INFO:	Input file is /tmp/tmpos9o7_en/files/a/d/3/dataset_ad372717-5464-4178-b45e-609785ffda51.dat
2024-10-24 13:57:08 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-10-24 13:57:08 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-10-24 13:57:08 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2024-10-24 13:57:08 INFO:	Running 1 job(s) on bbtools, starting at 10/24/2024 13:57:08
2024-10-24 13:57:10 INFO:	[bbtools]	1 of 1 task(s) completed
2024-10-24 13:57:10 INFO:	Running 1 job(s) on metaeuk, starting at 10/24/2024 13:57:10
2024-10-24 14:02:54 INFO:	[metaeuk]	1 of 1 task(s) completed
2024-10-24 14:02:54 INFO:	***** Run HMMER on gene sequences *****
2024-10-24 14:02:55 INFO:	Running 3354 job(s) on hmmsearch, starting at 10/24/2024 14:02:55
2024-10-24 14:03:25 INFO:	[hmmsearch]	336 of 3354 task(s) completed
2024-10-24 14:03:53 INFO:	[hmmsearch]	671 of 3354 task(s) completed
2024-10-24 14:04:20 INFO:	[hmmsearch]	1007 of 3354 task(s) completed
2024-10-24 14:04:47 INFO:	[hmmsearch]	1342 of 3354 task(s) completed
2024-10-24 14:05:14 INFO:	[hmmsearch]	1677 of 3354 task(s) completed
2024-10-24 14:05:40 INFO:	[hmmsearch]	2013 of 3354 task(s) completed
2024-10-24 14:06:06 INFO:	[hmmsearch]	2348 of 3354 task(s) completed
2024-10-24 14:06:31 INFO:	[hmmsearch]	2684 of 3354 task(s) completed
2024-10-24 14:06:58 INFO:	[hmmsearch]	3019 of 3354 task(s) completed
2024-10-24 14:07:26 INFO:	[hmmsearch]	3354 of 3354 task(s) completed
2024-10-24 14:07:26 INFO:	54 exons in total
2024-10-24 14:07:27 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-10-24 14:09:24 INFO:	Running 1 job(s) on metaeuk, starting at 10/24/2024 14:09:24
2024-10-24 14:16:58 INFO:	[metaeuk]	1 of 1 task(s) completed
2024-10-24 14:16:58 INFO:	***** Run HMMER on gene sequences *****
2024-10-24 14:16:58 INFO:	Running 3318 job(s) on hmmsearch, starting at 10/24/2024 14:16:58
2024-10-24 14:17:03 INFO:	[hmmsearch]	332 of 3318 task(s) completed
2024-10-24 14:17:08 INFO:	[hmmsearch]	664 of 3318 task(s) completed
2024-10-24 14:17:13 INFO:	[hmmsearch]	996 of 3318 task(s) completed
2024-10-24 14:17:17 INFO:	[hmmsearch]	1328 of 3318 task(s) completed
2024-10-24 14:17:22 INFO:	[hmmsearch]	1660 of 3318 task(s) completed
2024-10-24 14:17:27 INFO:	[hmmsearch]	1991 of 3318 task(s) completed
2024-10-24 14:17:32 INFO:	[hmmsearch]	2323 of 3318 task(s) completed
2024-10-24 14:17:37 INFO:	[hmmsearch]	2655 of 3318 task(s) completed
2024-10-24 14:17:42 INFO:	[hmmsearch]	2987 of 3318 task(s) completed
2024-10-24 14:17:46 INFO:	[hmmsearch]	3318 of 3318 task(s) completed
2024-10-24 14:17:47 INFO:	5 candidate overlapping regions found
2024-10-24 14:17:47 INFO:	62 exons in total
2024-10-24 14:17:47 INFO:	Results:	C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354	   

2024-10-24 14:17:47 INFO:	

    ---------------------------------------------------
    |Results from dataset vertebrata_odb10             |
    ---------------------------------------------------
    |C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354       |
    |36    Complete BUSCOs (C)                         |
    |35    Complete and single-copy BUSCOs (S)         |
    |1    Complete and duplicated BUSCOs (D)           |
    |15    Fragmented BUSCOs (F)                       |
    |3303    Missing BUSCOs (M)                        |
    |3354    Total BUSCO groups searched               |
    ---------------------------------------------------
2024-10-24 14:17:47 INFO:	BUSCO analysis done with WARNING(s). Total running time: 1240 seconds

***** Summary of warnings: *****
2024-10-24 13:57:08 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-10-24 13:57:08 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_genome_met

2024-10-24 14:17:47 INFO:	Results written in /tmp/tmpos9o7_en/job_working_directory/000/28/working/busco_galaxy
2024-10-24 14:17:47 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-10-24 14:17:47 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 140
drwxr-xr-x 5 1001 127  4096 Oct 24 13:57 busco_sequences
-rw-r--r-- 1 1001 127 76396 Oct 24 14:17 full_table.tsv
drwxr-xr-x 4 1001 127  4096 Oct 24 14:07 hmmer_output
drwxr-xr-x 4 1001 127  4096 Oct 24 14:17 metaeuk_output
-rw-r--r-- 1 1001 127 42380 Oct 24 14:17 missing_busco_list.tsv
-rw-r--r-- 1 1001 127  2952 Oct 24 14:17 short_summary.json
-rw-r--r-- 1 1001 127   968 Oct 24 14:17 short_summary.txt
2024-10-24 14:17:48 INFO:	****************** Start plot generation at 10/24/2024 14:17:48 ******************
2024-10-24 14:17:48 INFO:	Load data ...
2024-10-24 14:17:48 INFO:	Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-10-24 14:17:48 INFO:	Generate the R code ...
2024-10-24 14:17:48 INFO:	Run the R code ...
2024-10-24 14:17:50 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-10-24 14:17:50 INFO:	Plot generation done. Total running time: 2.235100507736206 seconds
2024-10-24 14:17:50 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "metaeuk"}}`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image"]`

Step 37: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmpos9o7_en/job_working_directory/000/29/outputs/dataset_bdb490dd-7b02-4c16-b5cf-4cbfde48419d.dat' -g     '#' 'Number of' '/tmp/tmpos9o7_en/files/f/1/1/dataset_f115811c-d28f-4341-a1c7-2b33d8642a43.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 38: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpos9o7_en/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmpos9o7_en/files/9/a/b/dataset_9ab9a254-e4f8-49d8-b02c-e0fbda6c157c.dat' --output='/tmp/tmpos9o7_en/job_working_directory/000/30/outputs/dataset_0188f853-b65c-42a6-a6c2-402f07017bab.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f1406fb9920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpos9o7_en/job_working_directory/000/31/configs/tmppbsxlkb4' '/tmp/tmpos9o7_en/files/0/1/8/dataset_0188f853-b65c-42a6-a6c2-402f07017bab.dat' > '/tmp/tmpos9o7_en/job_working_directory/000/31/outputs/dataset_fb218745-c984-4d43-9f97-65cf7a6e8efa.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb9920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmpos9o7_en/files/f/b/2/dataset_fb218745-c984-4d43-9f97-65cf7a6e8efa.dat > '/tmp/tmpos9o7_en/job_working_directory/000/32/outputs/dataset_c8d7da2c-6b60-4fab-8362-b1091ac4cc06.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb9920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpos9o7_en/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpos9o7_en/files/f/b/2/dataset_fb218745-c984-4d43-9f97-65cf7a6e8efa.dat' '/tmp/tmpos9o7_en/job_working_directory/000/33/outputs/dataset_246f7474-d373-43d3-b032-d9cb286ec19c.dat' '1' yes

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb9920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f1406fb9920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb9920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1971489", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmpos9o7_en/job_working_directory/000/42/configs/tmpmm7al9z4' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpos9o7_en/files/2/4/6/dataset_246f7474-d373-43d3-b032-d9cb286ec19c.dat' '/tmp/tmpos9o7_en/job_working_directory/000/42/outputs/dataset_7efb6112-38b4-4615-8a03-33503aa49563.dat'

Exit Code:

```
0
```

Standard Output:

c3/1971489
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1971489;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 83 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb9920e11efad514158eeee52ca"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1971489"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 39: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpos9o7_en/files/6/1/b/dataset_61bd5ccf-2a44-4829-9641-b34891f50007.dat' 'forward_input.bam' && ln -s '/tmp/tmpos9o7_en/files/3/6/4/dataset_3642ac5a-b369-4cf4-8909-54da5ba04d5e.dat' 'reverse_input.bam' && bellerophon --forward forward_input.bam --reverse reverse_input.bam --quality 20 --output 'merged_out.bam' --threads ${GALAXY_SLOTS:-1} && samtools sort --no-PG -O BAM -o '/tmp/tmpos9o7_en/job_working_directory/000/35/outputs/dataset_c6699f15-6c25-49fa-a550-b9f15a034c04.dat' -@ ${GALAXY_SLOTS:-1} merged_out.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 40: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpos9o7_en/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpos9o7_en/files/7/e/f/dataset_7efb6112-38b4-4615-8a03-33503aa49563.dat' 'c5,c6' T '/tmp/tmpos9o7_en/job_working_directory/000/43/outputs/dataset_3b9b7782-d3a5-4d4a-bd9c-8697f2dd736e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 5: Collection Hi-C forward reads:
- step_state: scheduled

Step 41: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpos9o7_en/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpos9o7_en/files/7/e/f/dataset_7efb6112-38b4-4615-8a03-33503aa49563.dat' 'c4,c7' T '/tmp/tmpos9o7_en/job_working_directory/000/44/outputs/dataset_6e9637e3-a449-41c5-b8d2-eecc367d772a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 42: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmpos9o7_en/files/c/6/6/dataset_c6699f15-6c25-49fa-a550-b9f15a034c04.dat' | PretextMap -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 83 sequences, sorted by length, descending. Filtering by minimum mapping quality 10

                                                                                
[PretextMap status] :: 10.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 10.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 15.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 20.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 25.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 30.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 35.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 40.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 45.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 50.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 55.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 60.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 65.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 70.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 75.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 80.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 85.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 90.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 95.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 100.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 105.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 109.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 114.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 119.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 125.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 130.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 135.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 139.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 144.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 149.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 154.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 159.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 164.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 169.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 174.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 179.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 184.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 190.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 195.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 199.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 204.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 209.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 214.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 219.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 224.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 229.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 234.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 239.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 245.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 250.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 255.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 260.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 265.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 270.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 275.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 280.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 285.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 290.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 294.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 300.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 305.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 310.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 314.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 640.0 k reads processed, 320.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 650.0 k reads processed, 325.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 660.0 k reads processed, 330.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 670.0 k reads processed, 335.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 680.0 k reads processed, 340.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 690.0 k reads processed, 345.0 k read-pairs mapped
[PretextMap status] :: Creating MipMaps...
[PretextMap status] :: Equalising contrast...
[PretextMap status] :: Compressing textures...

[PretextMap status] ::   1/528 (0.19%) texture blocks written to disk
[PretextMap status] ::   2/528 (0.38%) texture blocks written to disk
[PretextMap status] ::   3/528 (0.57%) texture blocks written to disk
[PretextMap status] ::   4/528 (0.76%) texture blocks written to disk
[PretextMap status] ::   5/528 (0.95%) texture blocks written to disk
[PretextMap status] ::   6/528 (1.14%) texture blocks written to disk
[PretextMap status] ::   7/528 (1.33%) texture blocks written to disk
[PretextMap status] ::   8/528 (1.52%) texture blocks written to disk
[PretextMap status] ::   9/528 (1.70%) texture blocks written to disk
[PretextMap status] ::  10/528 (1.89%) texture blocks written to disk
[PretextMap status] ::  11/528 (2.08%) texture blocks written to disk
[PretextMap status] ::  12/528 (2.27%) texture blocks written to disk
[PretextMap status] ::  13/528 (2.46%) texture blocks written to disk
[PretextMap status] ::  14/528 (2.65%) texture blocks written to disk
[PretextMap status] ::  15/528 (2.84%) texture blocks written to disk
[PretextMap status] ::  16/528 (3.03%) texture blocks written to disk
[PretextMap status] ::  17/528 (3.22%) texture blocks written to disk
[PretextMap status] ::  18/528 (3.41%) texture blocks written to disk
[PretextMap status] ::  19/528 (3.60%) texture blocks written to disk
[PretextMap status] ::  20/528 (3.79%) texture blocks written to disk
[PretextMap status] ::  21/528 (3.98%) texture blocks written to disk
[PretextMap status] ::  22/528 (4.17%) texture blocks written to disk
[PretextMap status] ::  23/528 (4.36%) texture blocks written to disk
[PretextMap status] ::  24/528 (4.55%) texture blocks written to disk
[PretextMap status] ::  25/528 (4.73%) texture blocks written to disk
[PretextMap status] ::  26/528 (4.92%) texture blocks written to disk
[PretextMap status] ::  27/528 (5.11%) texture blocks written to disk
[PretextMap status] ::  28/528 (5.30%) texture blocks written to disk
[PretextMap status] ::  29/528 (5.49%) texture blocks written to disk
[PretextMap status] ::  30/528 (5.68%) texture blocks written to disk
[PretextMap status] ::  31/528 (5.87%) texture blocks written to disk
[PretextMap status] ::  32/528 (6.06%) texture blocks written to disk
[PretextMap status] ::  33/528 (6.25%) texture blocks written to disk
[PretextMap status] ::  34/528 (6.44%) texture blocks written to disk
[PretextMap status] ::  35/528 (6.63%) texture blocks written to disk
[PretextMap status] ::  36/528 (6.82%) texture blocks written to disk
[PretextMap status] ::  37/528 (7.01%) texture blocks written to disk
[PretextMap status] ::  38/528 (7.20%) texture blocks written to disk
[PretextMap status] ::  39/528 (7.39%) texture blocks written to disk
[PretextMap status] ::  40/528 (7.58%) texture blocks written to disk
[PretextMap status] ::  41/528 (7.77%) texture blocks written to disk
[PretextMap status] ::  42/528 (7.95%) texture blocks written to disk
[PretextMap status] ::  43/528 (8.14%) texture blocks written to disk
[PretextMap status] ::  44/528 (8.33%) texture blocks written to disk
[PretextMap status] ::  45/528 (8.52%) texture blocks written to disk
[PretextMap status] ::  46/528 (8.71%) texture blocks written to disk
[PretextMap status] ::  47/528 (8.90%) texture blocks written to disk
[PretextMap status] ::  48/528 (9.09%) texture blocks written to disk
[PretextMap status] ::  49/528 (9.28%) texture blocks written to disk
[PretextMap status] ::  50/528 (9.47%) texture blocks written to disk
[PretextMap status] ::  51/528 (9.66%) texture blocks written to disk
[PretextMap status] ::  52/528 (9.85%) texture blocks written to disk
[PretextMap status] ::  53/528 (10.04%) texture blocks written to disk
[PretextMap status] ::  54/528 (10.23%) texture blocks written to disk
[PretextMap status] ::  55/528 (10.42%) texture blocks written to disk
[PretextMap status] ::  56/528 (10.61%) texture blocks written to disk
[PretextMap status] ::  57/528 (10.80%) texture blocks written to disk
[PretextMap status] ::  58/528 (10.98%) texture blocks written to disk
[PretextMap status] ::  59/528 (11.17%) texture blocks written to disk
[PretextMap status] ::  60/528 (11.36%) texture blocks written to disk
[PretextMap status] ::  61/528 (11.55%) texture blocks written to disk
[PretextMap status] ::  62/528 (11.74%) texture blocks written to disk
[PretextMap status] ::  63/528 (11.93%) texture blocks written to disk
[PretextMap status] ::  64/528 (12.12%) texture blocks written to disk
[PretextMap status] ::  65/528 (12.31%) texture blocks written to disk
[PretextMap status] ::  66/528 (12.50%) texture blocks written to disk
[PretextMap status] ::  67/528 (12.69%) texture blocks written to disk
[PretextMap status] ::  68/528 (12.88%) texture blocks written to disk
[PretextMap status] ::  69/528 (13.07%) texture blocks written to disk
[PretextMap status] ::  70/528 (13.26%) texture blocks written to disk
[PretextMap status] ::  71/528 (13.45%) texture blocks written to disk
[PretextMap status] ::  72/528 (13.64%) texture blocks written to disk
[PretextMap status] ::  73/528 (13.83%) texture blocks written to disk
[PretextMap status] ::  74/528 (14.02%) texture blocks written to disk
[PretextMap status] ::  75/528 (14.20%) texture blocks written to disk
[PretextMap status] ::  76/528 (14.39%) texture blocks written to disk
[PretextMap status] ::  77/528 (14.58%) texture blocks written to disk
[PretextMap status] ::  78/528 (14.77%) textu
..
:: 298/528 (56.44%) texture blocks written to disk
[PretextMap status] :: 299/528 (56.63%) texture blocks written to disk
[PretextMap status] :: 300/528 (56.82%) texture blocks written to disk
[PretextMap status] :: 301/528 (57.01%) texture blocks written to disk
[PretextMap status] :: 302/528 (57.20%) texture blocks written to disk
[PretextMap status] :: 303/528 (57.39%) texture blocks written to disk
[PretextMap status] :: 304/528 (57.58%) texture blocks written to disk
[PretextMap status] :: 305/528 (57.77%) texture blocks written to disk
[PretextMap status] :: 306/528 (57.95%) texture blocks written to disk
[PretextMap status] :: 307/528 (58.14%) texture blocks written to disk
[PretextMap status] :: 308/528 (58.33%) texture blocks written to disk
[PretextMap status] :: 309/528 (58.52%) texture blocks written to disk
[PretextMap status] :: 310/528 (58.71%) texture blocks written to disk
[PretextMap status] :: 311/528 (58.90%) texture blocks written to disk
[PretextMap status] :: 312/528 (59.09%) texture blocks written to disk
[PretextMap status] :: 313/528 (59.28%) texture blocks written to disk
[PretextMap status] :: 314/528 (59.47%) texture blocks written to disk
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Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 43: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpos9o7_en/files/c/6/6/dataset_c6699f15-6c25-49fa-a550-b9f15a034c04.dat' ./input.bam &&  bedtools bamtobed -bed12   -i ./input.bam > '/tmp/tmpos9o7_en/job_working_directory/000/37/outputs/dataset_f11c9f88-8747-45c9-aa03-0b4ac848ad27.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ed_score	`false`
option	`"-bed12"`
split	`false`
tag	`""`

Step 44: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpos9o7_en/job_working_directory/000/45/configs/tmp_on52z95' && Rscript '/tmp/tmpos9o7_en/job_working_directory/000/45/configs/tmp_on52z95'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpos9o7_en/files/3/b/9/dataset_3b9b7782-d3a5-4d4a-bd9c-8697f2dd736e.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpos9o7_en/job_working_directory/000/45/outputs/dataset_4f9953c9-7245-43e0-9be0-91aea09fcaa9.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"x"`
xplot	`"1"`
ylab	`"Nx (Mb)"`
yplot	`"2"`

Step 45: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpos9o7_en/job_working_directory/000/46/configs/tmpz9q9fpvt' && Rscript '/tmp/tmpos9o7_en/job_working_directory/000/46/configs/tmpz9q9fpvt'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpos9o7_en/files/6/e/9/dataset_6e9637e3-a449-41c5-b8d2-eecc367d772a.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpos9o7_en/job_working_directory/000/46/outputs/dataset_07ee5ca9-3c4f-44bf-bafe-78e36828d3db.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"1"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"2"`

Step 46: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmpos9o7_en/files/e/7/6/dataset_e76d8af4-ba0d-485c-864c-1bbf9a70754a.dat -f png -r 1000 -c 5 --sequences '=full' --minTexels 64 --gridSize 1 --gridColour black '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmpos9o7_en/files/e/7/6/dataset_e76d8af4-ba0d-485c-864c-1bbf9a70754a.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 1000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 1 pixel
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 0, "gridcolor": "black", "gridsize": "1", "showGrid": "yes"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 47: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

( LC_ALL=C  sort   --stable -t '	'  -k '4,4'  ) < '/tmp/tmpos9o7_en/files/f/1/1/dataset_f11c9f88-8747-45c9-aa03-0b4ac848ad27.dat' > '/tmp/tmpos9o7_en/job_working_directory/000/39/outputs/dataset_ce3b0454-7e54-4173-baf3-b81a9d986b7b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
chromInfo	`"/tmp/tmpos9o7_en/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`"0"`
ignore_case	`false`
sortkeys	`[{"__index__": 0, "column": "4", "order": "", "style": ""}]`
unique	`false`

Step 48: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f1406fb8920e11efad514158eeee52ca"`
input	`{"values": [{"id": 9, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 6: Collection Hi-C reverse reads:
- step_state: scheduled
Step 7: Database for Busco Lineage:
- step_state: scheduled
Step 8: Lineage:
- step_state: scheduled
Step 9: Restriction enzymes:
- step_state: scheduled
Step 10: Estimated genome size - Parameter File:
- step_state: scheduled

Other invocation details
- history_id
  - 2f4fb55c74170b7c
- history_state
  - ok
- invocation_id
  - 2f4fb55c74170b7c
- invocation_state
  - scheduled
- workflow_id
  - b37d9757965262e7

gxydevbot · 2024-11-04T04:27:46Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-11-11T04:34:37Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-11-18T04:47:04Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-11-25T04:57:32Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-12-02T04:37:51Z

There are new updates, if you want to integrate them, close the PR and delete branch.

github-actions · 2024-12-03T17:59:49Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '38' (Hi-C forward reads) is not optional and no input provided.","err_code":0}

github-actions · 2024-12-03T18:00:37Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '38' (Hi-C forward reads) is not optional and no input provided.","err_code":0}

github-actions · 2024-12-03T18:00:51Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '38' (Hi-C forward reads) is not optional and no input provided.","err_code":0}

github-actions · 2024-12-13T15:27:10Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Final state of invocation f4c424bdaadaf0c6 is [failed]. Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 7 requires a dataset created by step 6, but dataset entered a failed state.

Steps

Step 1: Input GFA:
- step_state: scheduled
Step 2: Haplotype:
- step_state: scheduled
Step 11: Sequence graph:
- step_state: scheduled

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "$&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "hap1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 13: __SORTLIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
input	`{"values": [{"id": 1, "src": "hdca"}]}`
sort_type	`{"__current_case__": 0, "sort_type": "alpha"}`

Step 14: __SORTLIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
input	`{"values": [{"id": 2, "src": "hdca"}]}`
sort_type	`{"__current_case__": 0, "sort_type": "alpha"}`

Step 15: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpu89ik0ds/files/1/9/8/dataset_19871612-f99e-4017-96b7-f0253807d20e.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 84
Total scaffold length: 1982895
Average scaffold length: 23605.89
Scaffold N50: 20934
Scaffold auN: 33899.67
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 84
Total contig length: 1982895
Average contig length: 23605.89
Contig N50: 20934
Contig auN: 33899.67
Contig L50: 30
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 606458:383991:386001:606445
GC content %: 38.83
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 84
# edges: 4
Average degree: 0.05
# connected components: 1
Largest connected component length: 94650
# dead ends: 165
# disconnected components: 81
Total length disconnected components: 1888245
# separated components: 82
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 17: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	`{"__current_case__": 1, "input_1": {"values": [{"id": 3, "src": "dce"}]}, "input_2": {"values": [{"id": 4, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired"}`
other_trimming_options	`{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`None`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 18: Pick forward reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 5, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 3, "src": "dce"}]}}]}}`

Step 19: Pick reverse reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 6, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 4, "src": "dce"}]}}]}}`

Step 20: Hi-C Forward reads:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

(   cat "/tmp/tmpu89ik0ds/files/b/2/1/dataset_b21f2f76-c5e7-4389-878e-e889fe8aa4df.dat" ;   ) > /tmp/tmpu89ik0ds/job_working_directory/000/13/outputs/dataset_3cfb74b1-2aa9-4c12-b036-397f4e9470da.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 3: Hi-C forward reads:
- step_state: scheduled

Step 21: Hi-C Reverse reads:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

(   cat "/tmp/tmpu89ik0ds/files/9/c/b/dataset_9cb761d4-39b1-4e75-826d-266a8eec69dc.dat" ;   ) > /tmp/tmpu89ik0ds/job_working_directory/000/14/outputs/dataset_30f8f2c5-c3e0-4c36-bd27-4d205225b055.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 14, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 15, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function	`{"__current_case__": 0, "agp": null, "bfile": {"values": [{"id": 18, "src": "hda"}]}, "enzyme_conditional": {"__current_case__": 1, "enzyme_options": "preconfigured", "preconfigured_enzymes": "arima2"}, "fasta": {"values": [{"id": 9, "src": "hda"}]}, "function_select": "yahs", "length": null, "no_contig_ec": true, "no_scaffold_ec": false, "quality": null, "res": ""}`
log_out	`true`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 1, "showGrid": "no"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "scaffold_[0-9]*", "global": true, "is_regex": true, "replace_pattern": "$&.hap1", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": true}]`

Step 29: Unlabelled step:
- step_state: new

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 2, "agp_to_path": {"values": [{"id": 23, "src": "hda"}]}, "discover_paths": false, "selector": "scaffolding"}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 4: Hi-C reverse reads:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 33: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "s", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 34: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 14, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 25, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 15, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 25, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 36: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "metaeuk"}}`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image"]`

Step 37: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 38: Unlabelled step:

step_state: new

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6c301403b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301403b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301403b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301403b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6c301403b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: Unlabelled step:
- step_state: new
Step 8: Unlabelled step:
- step_state: new

Step 39: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 40: Unlabelled step:
- step_state: new
Step 5: Trim Hi-C Data?:
- step_state: scheduled
Step 41: Unlabelled step:
- step_state: new

Step 42: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 43: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ed_score	`false`
option	`"-bed12"`
split	`false`
tag	`""`

Step 44: Nx Plot:
- step_state: new
Step 45: Size Plot:
- step_state: new

Step 46: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 0, "gridcolor": "black", "gridsize": "1", "showGrid": "yes"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 47: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6c301402b96611ef899e6045bda8ceff"`
chromInfo	`"/tmp/tmpu89ik0ds/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`"0"`
ignore_case	`false`
sortkeys	`[{"__index__": 0, "column": "4", "order": "", "style": ""}]`
unique	`false`

Step 48: Unlabelled step:
- step_state: new
Step 6: Database for Busco Lineage:
- step_state: scheduled
Step 7: Lineage:
- step_state: scheduled
Step 8: Restriction enzymes:
- step_state: scheduled
Step 9: Estimated genome size - Parameter File:
- step_state: scheduled
Step 10: SAK input file:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation f4c424bdaadaf0c6 is [failed]. Failed to run workflow, at least one job is in [error] state.
- history_id
  - f4c424bdaadaf0c6
- history_state
  - error
- invocation_id
  - f4c424bdaadaf0c6
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': 5, 'hda_id': '7c009495278a0698', 'reason': 'dataset_failed', 'workflow_step_id': 6}]
- workflow_id
  - b82a710b3d419cfe

github-actions · 2024-12-13T18:04:17Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Scaffolding-HiC-VGP8.ga_0

Execution Problem:

Final state of invocation 07e926898912262c is [failed]. Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 7 requires a dataset created by step 6, but dataset entered a failed state.

Steps

Step 1: Input GFA:
- step_state: scheduled
Step 2: Haplotype:
- step_state: scheduled
Step 11: Sequence graph:
- step_state: scheduled

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "$&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "hap1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 13: __SORTLIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
input	`{"values": [{"id": 1, "src": "hdca"}]}`
sort_type	`{"__current_case__": 0, "sort_type": "alpha"}`

Step 14: __SORTLIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
input	`{"values": [{"id": 2, "src": "hdca"}]}`
sort_type	`{"__current_case__": 0, "sort_type": "alpha"}`

Step 15: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp43os6b5s/files/e/2/d/dataset_e2d52faa-4180-4121-a576-9067fe02d817.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 84
Total scaffold length: 1982895
Average scaffold length: 23605.89
Scaffold N50: 20934
Scaffold auN: 33899.67
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 84
Total contig length: 1982895
Average contig length: 23605.89
Contig N50: 20934
Contig auN: 33899.67
Contig L50: 30
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 606458:383991:386001:606445
GC content %: 38.83
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 84
# edges: 4
Average degree: 0.05
# connected components: 1
Largest connected component length: 94650
# dead ends: 165
# disconnected components: 81
Total length disconnected components: 1888245
# separated components: 82
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 17: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	`{"__current_case__": 1, "input_1": {"values": [{"id": 3, "src": "dce"}]}, "input_2": {"values": [{"id": 4, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired"}`
other_trimming_options	`{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`None`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 18: Pick forward reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 5, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 3, "src": "dce"}]}}]}}`

Step 19: Pick reverse reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 6, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 4, "src": "dce"}]}}]}}`

Step 20: Hi-C Forward reads:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

(   cat "/tmp/tmp43os6b5s/files/d/2/f/dataset_d2f5be6d-fe62-4738-a6b5-aef432d6c20f.dat" ;   ) > /tmp/tmp43os6b5s/job_working_directory/000/13/outputs/dataset_1265560c-701d-4e40-8263-1100b4ae1a7c.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 3: Hi-C forward reads:
- step_state: scheduled

Step 21: Hi-C Reverse reads:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

(   cat "/tmp/tmp43os6b5s/files/6/5/6/dataset_656199dc-f80e-4d18-8d8a-fc0050178231.dat" ;   ) > /tmp/tmp43os6b5s/job_working_directory/000/14/outputs/dataset_659c3856-2777-4ae8-ac4d-e4596bda2f3d.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 14, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 15, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function	`{"__current_case__": 0, "agp": null, "bfile": {"values": [{"id": 18, "src": "hda"}]}, "enzyme_conditional": {"__current_case__": 1, "enzyme_options": "preconfigured", "preconfigured_enzymes": "arima2"}, "fasta": {"values": [{"id": 9, "src": "hda"}]}, "function_select": "yahs", "length": null, "no_contig_ec": true, "no_scaffold_ec": false, "quality": null, "res": ""}`
log_out	`true`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 1, "showGrid": "no"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "scaffold_[0-9]*", "global": true, "is_regex": true, "replace_pattern": "$&.hap1", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": true}]`

Step 29: Unlabelled step:
- step_state: new

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 2, "agp_to_path": {"values": [{"id": 23, "src": "hda"}]}, "discover_paths": false, "selector": "scaffolding"}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 4: Hi-C reverse reads:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 33: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "s", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 34: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 14, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 25, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 15, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 25, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 36: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "metaeuk"}}`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image"]`

Step 37: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 38: Unlabelled step:

step_state: new

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5fd207e1b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e1b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e1b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e1b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5fd207e1b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: Unlabelled step:
- step_state: new
Step 8: Unlabelled step:
- step_state: new

Step 39: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 40: Unlabelled step:
- step_state: new
Step 5: Trim Hi-C Data?:
- step_state: scheduled
Step 41: Unlabelled step:
- step_state: new

Step 42: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 43: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ed_score	`false`
option	`"-bed12"`
split	`false`
tag	`""`

Step 44: Nx Plot:
- step_state: new
Step 45: Size Plot:
- step_state: new

Step 46: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 0, "gridcolor": "black", "gridsize": "1", "showGrid": "yes"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 47: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5fd207e0b97c11ef899e7c1e526d504e"`
chromInfo	`"/tmp/tmp43os6b5s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`"0"`
ignore_case	`false`
sortkeys	`[{"__index__": 0, "column": "4", "order": "", "style": ""}]`
unique	`false`

Step 48: Unlabelled step:
- step_state: new
Step 6: Database for Busco Lineage:
- step_state: scheduled
Step 7: Lineage:
- step_state: scheduled
Step 8: Restriction enzymes:
- step_state: scheduled
Step 9: Estimated genome size - Parameter File:
- step_state: scheduled
Step 10: SAK input file:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation 07e926898912262c is [failed]. Failed to run workflow, at least one job is in [error] state.
- history_id
  - 07e926898912262c
- history_state
  - error
- invocation_id
  - 07e926898912262c
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': 5, 'hda_id': '1e0bbbcf0172bb3b', 'reason': 'dataset_failed', 'workflow_step_id': 6}]
- workflow_id
  - 794950c43e9b511d

gxydevbot · 2024-12-16T04:54:12Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-12-23T04:46:17Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-12-30T04:31:31Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2025-01-06T04:34:07Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2025-01-13T04:35:16Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2025-01-20T04:29:08Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2025-01-27T04:36:49Z

There are new updates, if you want to integrate them, close the PR and delete branch.

github-actions · 2025-01-31T23:56:01Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	1
Error	0
Failure	0
Skipped	0

Passed Tests

✅ Scaffolding-HiC-VGP8.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Input GFA:
- step_state: scheduled
Step 2: Haplotype:
- step_state: scheduled
Step 11: Sequence graph:
- step_state: scheduled

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "$&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "hap1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 13: __SORTLIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
input	`{"values": [{"id": 1, "src": "hdca"}]}`
sort_type	`{"__current_case__": 0, "sort_type": "alpha"}`

Step 14: __SORTLIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
input	`{"values": [{"id": 2, "src": "hdca"}]}`
sort_type	`{"__current_case__": 0, "sort_type": "alpha"}`

Step 15: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp72uiczf6/files/9/2/8/dataset_92887699-38f0-4d06-9192-b81952f60d84.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 84
Total scaffold length: 1982895
Average scaffold length: 23605.89
Scaffold N50: 20934
Scaffold auN: 33899.67
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 84
Total contig length: 1982895
Average contig length: 23605.89
Contig N50: 20934
Contig auN: 33899.67
Contig L50: 30
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 606458:383991:386001:606445
GC content %: 38.83
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 84
# edges: 4
Average degree: 0.05
# connected components: 1
Largest connected component length: 94650
# dead ends: 165
# disconnected components: 81
Total length disconnected components: 1888245
# separated components: 82
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 17: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	`{"__current_case__": 1, "input_1": {"values": [{"id": 3, "src": "dce"}]}, "input_2": {"values": [{"id": 4, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired"}`
other_trimming_options	`{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`None`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 18: Pick forward reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 5, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 3, "src": "dce"}]}}]}}`

Step 19: Pick reverse reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 6, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 4, "src": "dce"}]}}]}}`

Step 20: Hi-C Forward reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

(   cat "/tmp/tmp72uiczf6/files/d/b/4/dataset_db45639b-b472-42d8-a880-307b1021482f.dat" ;   ) > /tmp/tmp72uiczf6/job_working_directory/000/13/outputs/dataset_a76a5328-6850-4fa9-86a6-90691dc1c7bb.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 3: Hi-C forward reads:
- step_state: scheduled

Step 21: Hi-C Reverse reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

(   cat "/tmp/tmp72uiczf6/files/2/c/f/dataset_2cf87e40-83ce-461f-aacd-e6015f19a0a9.dat" ;   ) > /tmp/tmp72uiczf6/job_working_directory/000/14/outputs/dataset_844a71fb-161e-4be5-8bd0-23d749182684.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp72uiczf6/files/e/f/7/dataset_ef772890-3dde-4adb-82b3-5f8615b5c2b8.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmp72uiczf6/files/a/7/6/dataset_a76a5328-6850-4fa9-86a6-90691dc1c7bb.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp72uiczf6/job_working_directory/000/15/outputs/dataset_b11799b0-4f29-427f-9946-54660c712953.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 156447625
ref seq len = 3965790
binary seq ticks = 93324193
build suffix-array ticks = 629034731
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 199457104
Total time taken: 0.4545
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 3041008
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000037, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000037 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000053, nseq: 100108
	[0000][ M::kt_pipeline] read 100108 sequences (10000053 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 5.053 CPU sec, 5.053 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000072, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000072 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100108 reads in 5.229 CPU sec, 5.310 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000203, nseq: 100132
	[0000][ M::kt_pipeline] read 100132 sequences (10000203 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 5.253 CPU sec, 5.336 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000073, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000073 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100132 reads in 5.070 CPU sec, 5.151 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000141, nseq: 100166
	[0000][ M::kt_pipeline] read 100166 sequences (10000141 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 5.153 CPU sec, 5.231 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000104, nseq: 118598
	[0000][ M::kt_pipeline] read 118598 sequences (10000104 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100166 reads in 5.205 CPU sec, 5.281 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000109, nseq: 151884
	[0000][ M::kt_pipeline] read 151884 sequences (10000109 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118598 reads in 5.181 CPU sec, 5.260 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000126, nseq: 151908
	[0000][ M::kt_pipeline] read 151908 sequences (10000126 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151884 reads in 4.827 CPU sec, 4.914 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151908 reads in 4.869 CPU sec, 4.971 real sec
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000007, nseq: 151868
	[0000][ M::kt_pipeline] read 151868 sequences (10000007 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 4.854 CPU sec, 4.945 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000077, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000077 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151868 reads in 4.992 CPU sec, 5.100 real sec
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000024, nseq: 127818
	[0000][ M::kt_pipeline] read 127818 sequences (10000024 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 4.981 CPU sec, 5.078 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000071, nseq: 98956
	[0000][ M::kt_pipeline] read 98956 sequences (10000071 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127818 reads in 6.481 CPU sec, 6.577 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000004, nseq: 145156
	[0000][ M::kt_pipeline] read 145156 sequences (10000004 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98956 reads in 8.646 CPU sec, 8.736 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3496096, nseq: 53016
	[0000][ M::kt_pipeline] read 53016 sequences (3496096 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145156 reads in 7.348 CPU sec, 7.425 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 53016 reads in 2.597 CPU sec, 2.692 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.611169 MHz
Runtime profile:

	Time taken for main_mem function: 87.31 sec

	IO times (sec) :
	Reading IO time (reads) avg: 5.26, (5.26, 5.26)
	Writing IO time (SAM) avg: 3.67, (3.67, 3.67)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.00, (0.00, 0.00)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 87.30
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 87.05, (87.05, 87.05)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 7.68, (7.68, 7.68)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 79.37, (79.37, 79.37)
		SMEM compute avg: 25.51, (25.51, 25.51)
		SAL compute avg: 16.92, (16.92, 16.92)
				MEM_SA avg: 8.35, (8.35, 8.35)

		BSW time, avg: 31.98, (31.98, 31.98)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[3041008] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 14, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp72uiczf6/files/e/f/7/dataset_ef772890-3dde-4adb-82b3-5f8615b5c2b8.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmp72uiczf6/files/8/4/4/dataset_844a71fb-161e-4be5-8bd0-23d749182684.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp72uiczf6/job_working_directory/000/16/outputs/dataset_8d44ac19-7a29-4624-869b-b5af9f6a336f.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 155011966
ref seq len = 3965790
binary seq ticks = 67954450
build suffix-array ticks = 581821125
pos: 495724, ref_seq_len__: 495723
build fm-index ticks = 203797639
Total time taken: 0.4268
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3965791
* sentinel-index: 3041008
* Count:
0,	1
1,	1212904
2,	1982896
3,	2752888
4,	3965791

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3965790 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000036, nseq: 100212
	[0000][ M::kt_pipeline] read 100212 sequences (10000036 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000140, nseq: 100074
	[0000][ M::kt_pipeline] read 100074 sequences (10000140 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100212 reads in 5.158 CPU sec, 5.163 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000066, nseq: 100106
	[0000][ M::kt_pipeline] read 100106 sequences (10000066 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100074 reads in 5.266 CPU sec, 5.356 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000070, nseq: 100180
	[0000][ M::kt_pipeline] read 100180 sequences (10000070 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100106 reads in 5.211 CPU sec, 5.294 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000000, nseq: 100202
	[0000][ M::kt_pipeline] read 100202 sequences (10000000 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100180 reads in 5.341 CPU sec, 5.421 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000132, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000132 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100202 reads in 5.163 CPU sec, 5.238 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 118588
	[0000][ M::kt_pipeline] read 118588 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 5.178 CPU sec, 5.258 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000125, nseq: 151900
	[0000][ M::kt_pipeline] read 151900 sequences (10000125 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118588 reads in 5.151 CPU sec, 5.245 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000005, nseq: 151874
	[0000][ M::kt_pipeline] read 151874 sequences (10000005 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151900 reads in 4.801 CPU sec, 4.899 real sec
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151904
	[0000][ M::kt_pipeline] read 151904 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151874 reads in 4.735 CPU sec, 4.834 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151896
	[0000][ M::kt_pipeline] read 151896 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151904 reads in 4.862 CPU sec, 4.960 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000130, nseq: 151906
	[0000][ M::kt_pipeline] read 151906 sequences (10000130 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151896 reads in 5.008 CPU sec, 5.115 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 127808
	[0000][ M::kt_pipeline] read 127808 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151906 reads in 4.900 CPU sec, 4.994 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000028, nseq: 98948
	[0000][ M::kt_pipeline] read 98948 sequences (10000028 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127808 reads in 6.435 CPU sec, 6.531 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000026, nseq: 145218
	[0000][ M::kt_pipeline] read 145218 sequences (10000026 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98948 reads in 8.462 CPU sec, 8.551 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3489223, nseq: 52906
	[0000][ M::kt_pipeline] read 52906 sequences (3489223 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145218 reads in 7.283 CPU sec, 7.363 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 52906 reads in 2.639 CPU sec, 2.733 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.618474 MHz
Runtime profile:

	Time taken for main_mem function: 87.18 sec

	IO times (sec) :
	Reading IO time (reads) avg: 4.87, (4.87, 4.87)
	Writing IO time (SAM) avg: 3.90, (3.90, 3.90)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 87.17
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 86.95, (86.95, 86.95)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 7.75, (7.75, 7.75)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 79.20, (79.20, 79.20)
		SMEM compute avg: 25.54, (25.54, 25.54)
		SAL compute avg: 16.56, (16.56, 16.56)
				MEM_SA avg: 7.88, (7.88, 7.88)

		BSW time, avg: 32.49, (32.49, 32.49)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3965790
count = 0, 1212903, 1982895, 2752887, 3965790
BWT[3041008] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61965

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 15, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp72uiczf6/files/b/1/1/dataset_b11799b0-4f29-427f-9946-54660c712953.dat' 'forward_input.bam' && ln -s '/tmp/tmp72uiczf6/files/8/d/4/dataset_8d44ac19-7a29-4624-869b-b5af9f6a336f.dat' 'reverse_input.bam' && bellerophon --forward forward_input.bam --reverse reverse_input.bam --quality 20 --output 'merged_out.bam' --threads ${GALAXY_SLOTS:-1} && samtools sort --no-PG -O BAM -o '/tmp/tmp72uiczf6/job_working_directory/000/17/outputs/dataset_7770103d-bd3f-415c-93ef-0bcf1d84abfc.dat' -@ ${GALAXY_SLOTS:-1} merged_out.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmp72uiczf6/files/7/7/7/dataset_7770103d-bd3f-415c-93ef-0bcf1d84abfc.dat' | PretextMap -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 84 sequences, sorted by length, descending. Filtering by minimum mapping quality 10

                                                                                
[PretextMap status] :: 10.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 10.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 15.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 20.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 25.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 30.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 35.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 40.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 45.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 50.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 55.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 60.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 65.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 70.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 75.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 80.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 85.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 90.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 95.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 100.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 104.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 109.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 114.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 119.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 124.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 129.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 134.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 139.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 145.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 150.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 154.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 159.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 165.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 170.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 175.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 180.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 185.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 190.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 195.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 200.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 205.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 210.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 215.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 220.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 225.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 230.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 235.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 240.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 245.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 250.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 255.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 260.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 265.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 270.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 275.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 280.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 285.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 290.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 295.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 300.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 305.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 310.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 315.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 640.0 k reads processed, 320.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 650.0 k reads processed, 325.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 660.0 k reads processed, 330.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 670.0 k reads processed, 335.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 680.0 k reads processed, 340.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 690.0 k reads processed, 345.0 k read-pairs mapped
[PretextMap status] :: Creating MipMaps...
[PretextMap status] :: Equalising contrast...
[PretextMap status] :: Compressing textures...

[PretextMap status] ::   1/528 (0.19%) texture blocks written to disk
[PretextMap status] ::   2/528 (0.38%) texture blocks written to disk
[PretextMap status] ::   3/528 (0.57%) texture blocks written to disk
[PretextMap status] ::   4/528 (0.76%) texture blocks written to disk
[PretextMap status] ::   5/528 (0.95%) texture blocks written to disk
[PretextMap status] ::   6/528 (1.14%) texture blocks written to disk
[PretextMap status] ::   7/528 (1.33%) texture blocks written to disk
[PretextMap status] ::   8/528 (1.52%) texture blocks written to disk
[PretextMap status] ::   9/528 (1.70%) texture blocks written to disk
[PretextMap status] ::  10/528 (1.89%) texture blocks written to disk
[PretextMap status] ::  11/528 (2.08%) texture blocks written to disk
[PretextMap status] ::  12/528 (2.27%) texture blocks written to disk
[PretextMap status] ::  13/528 (2.46%) texture blocks written to disk
[PretextMap status] ::  14/528 (2.65%) texture blocks written to disk
[PretextMap status] ::  15/528 (2.84%) texture blocks written to disk
[PretextMap status] ::  16/528 (3.03%) texture blocks written to disk
[PretextMap status] ::  17/528 (3.22%) texture blocks written to disk
[PretextMap status] ::  18/528 (3.41%) texture blocks written to disk
[PretextMap status] ::  19/528 (3.60%) texture blocks written to disk
[PretextMap status] ::  20/528 (3.79%) texture blocks written to disk
[PretextMap status] ::  21/528 (3.98%) texture blocks written to disk
[PretextMap status] ::  22/528 (4.17%) texture blocks written to disk
[PretextMap status] ::  23/528 (4.36%) texture blocks written to disk
[PretextMap status] ::  24/528 (4.55%) texture blocks written to disk
[PretextMap status] ::  25/528 (4.73%) texture blocks written to disk
[PretextMap status] ::  26/528 (4.92%) texture blocks written to disk
[PretextMap status] ::  27/528 (5.11%) texture blocks written to disk
[PretextMap status] ::  28/528 (5.30%) texture blocks written to disk
[PretextMap status] ::  29/528 (5.49%) texture blocks written to disk
[PretextMap status] ::  30/528 (5.68%) texture blocks written to disk
[PretextMap status] ::  31/528 (5.87%) texture blocks written to disk
[PretextMap status] ::  32/528 (6.06%) texture blocks written to disk
[PretextMap status] ::  33/528 (6.25%) texture blocks written to disk
[PretextMap status] ::  34/528 (6.44%) texture blocks written to disk
[PretextMap status] ::  35/528 (6.63%) texture blocks written to disk
[PretextMap status] ::  36/528 (6.82%) texture blocks written to disk
[PretextMap status] ::  37/528 (7.01%) texture blocks written to disk
[PretextMap status] ::  38/528 (7.20%) texture blocks written to disk
[PretextMap status] ::  39/528 (7.39%) texture blocks written to disk
[PretextMap status] ::  40/528 (7.58%) texture blocks written to disk
[PretextMap status] ::  41/528 (7.77%) texture blocks written to disk
[PretextMap status] ::  42/528 (7.95%) texture blocks written to disk
[PretextMap status] ::  43/528 (8.14%) texture blocks written to disk
[PretextMap status] ::  44/528 (8.33%) texture blocks written to disk
[PretextMap status] ::  45/528 (8.52%) texture blocks written to disk
[PretextMap status] ::  46/528 (8.71%) texture blocks written to disk
[PretextMap status] ::  47/528 (8.90%) texture blocks written to disk
[PretextMap status] ::  48/528 (9.09%) texture blocks written to disk
[PretextMap status] ::  49/528 (9.28%) texture blocks written to disk
[PretextMap status] ::  50/528 (9.47%) texture blocks written to disk
[PretextMap status] ::  51/528 (9.66%) texture blocks written to disk
[PretextMap status] ::  52/528 (9.85%) texture blocks written to disk
[PretextMap status] ::  53/528 (10.04%) texture blocks written to disk
[PretextMap status] ::  54/528 (10.23%) texture blocks written to disk
[PretextMap status] ::  55/528 (10.42%) texture blocks written to disk
[PretextMap status] ::  56/528 (10.61%) texture blocks written to disk
[PretextMap status] ::  57/528 (10.80%) texture blocks written to disk
[PretextMap status] ::  58/528 (10.98%) texture blocks written to disk
[PretextMap status] ::  59/528 (11.17%) texture blocks written to disk
[PretextMap status] ::  60/528 (11.36%) texture blocks written to disk
[PretextMap status] ::  61/528 (11.55%) texture blocks written to disk
[PretextMap status] ::  62/528 (11.74%) texture blocks written to disk
[PretextMap status] ::  63/528 (11.93%) texture blocks written to disk
[PretextMap status] ::  64/528 (12.12%) texture blocks written to disk
[PretextMap status] ::  65/528 (12.31%) texture blocks written to disk
[PretextMap status] ::  66/528 (12.50%) texture blocks written to disk
[PretextMap status] ::  67/528 (12.69%) texture blocks written to disk
[PretextMap status] ::  68/528 (12.88%) texture blocks written to disk
[PretextMap status] ::  69/528 (13.07%) texture blocks written to disk
[PretextMap status] ::  70/528 (13.26%) texture blocks written to disk
[PretextMap status] ::  71/528 (13.45%) texture blocks written to disk
[PretextMap status] ::  72/528 (13.64%) texture blocks written to disk
[PretextMap status] ::  73/528 (13.83%) texture blocks written to disk
[PretextMap status] ::  74/528 (14.02%) texture blocks written to disk
[PretextMap status] ::  75/528 (14.20%) texture blocks written to disk
[PretextMap status] ::  76/528 (14.39%) texture blocks written to disk
[PretextMap status] ::  77/528 (14.58%) texture blocks written to disk
[PretextMap status] ::  78/528 (14.77%) textu
..
:: 298/528 (56.44%) texture blocks written to disk
[PretextMap status] :: 299/528 (56.63%) texture blocks written to disk
[PretextMap status] :: 300/528 (56.82%) texture blocks written to disk
[PretextMap status] :: 301/528 (57.01%) texture blocks written to disk
[PretextMap status] :: 302/528 (57.20%) texture blocks written to disk
[PretextMap status] :: 303/528 (57.39%) texture blocks written to disk
[PretextMap status] :: 304/528 (57.58%) texture blocks written to disk
[PretextMap status] :: 305/528 (57.77%) texture blocks written to disk
[PretextMap status] :: 306/528 (57.95%) texture blocks written to disk
[PretextMap status] :: 307/528 (58.14%) texture blocks written to disk
[PretextMap status] :: 308/528 (58.33%) texture blocks written to disk
[PretextMap status] :: 309/528 (58.52%) texture blocks written to disk
[PretextMap status] :: 310/528 (58.71%) texture blocks written to disk
[PretextMap status] :: 311/528 (58.90%) texture blocks written to disk
[PretextMap status] :: 312/528 (59.09%) texture blocks written to disk
[PretextMap status] :: 313/528 (59.28%) texture blocks written to disk
[PretextMap status] :: 314/528 (59.47%) texture blocks written to disk
[PretextMap status] :: 315/528 (59.66%) texture blocks written to disk
[PretextMap status] :: 316/528 (59.85%) texture blocks written to disk
[PretextMap status] :: 317/528 (60.04%) texture blocks written to disk
[PretextMap status] :: 318/528 (60.23%) texture blocks written to disk
[PretextMap status] :: 319/528 (60.42%) texture blocks written to disk
[PretextMap status] :: 320/528 (60.61%) texture blocks written to disk
[PretextMap status] :: 321/528 (60.80%) texture blocks written to disk
[PretextMap status] :: 322/528 (60.98%) texture blocks written to disk
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Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp72uiczf6/files/e/f/7/dataset_ef772890-3dde-4adb-82b3-5f8615b5c2b8.dat' input.fasta && ln -s '/tmp/tmp72uiczf6/files/7/7/7/dataset_7770103d-bd3f-415c-93ef-0bcf1d84abfc.dat' input.bam && samtools faidx input.fasta && mkdir initial_break agp_out agp_break final_outs && yahs --no-mem-check input.fasta input.bam -e 'GATC,GANTC,CTNAG,TTAA' --no-contig-ec  -o yahs_out 2> output.log && ls -lah && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/yahs/ff4031bfaa22/yahs/move_files.py' && ls -lah ./*

Exit Code:

```
0
```

Standard Output:

total 8M     
drwxr-xr-x    6 1001     118         4.0K Jan 31 22:48 .
drwxr-xr-x   12 1001     118         4.0K Jan 31 22:48 ..
drwxr-xr-x    2 1001     118         4.0K Jan 31 22:48 agp_break
drwxr-xr-x    2 1001     118         4.0K Jan 31 22:48 agp_out
drwxr-xr-x    2 1001     118         4.0K Jan 31 22:48 final_outs
drwxr-xr-x    2 1001     118         4.0K Jan 31 22:48 initial_break
lrwxrwxrwx    1 1001     118           77 Jan 31 22:48 input.bam -> /tmp/tmp72uiczf6/files/7/7/7/dataset_7770103d-bd3f-415c-93ef-0bcf1d84abfc.dat
lrwxrwxrwx    1 1001     118           77 Jan 31 22:48 input.fasta -> /tmp/tmp72uiczf6/files/e/f/7/dataset_ef772890-3dde-4adb-82b3-5f8615b5c2b8.dat
-rw-r--r--    1 1001     118         3.5K Jan 31 22:48 input.fasta.fai
-rw-r--r--    1 1001     118         5.1K Jan 31 22:48 output.log
-rw-r--r--    1 1001     118         5.6M Jan 31 22:48 yahs_out.bin
-rw-r--r--    1 1001     118         4.2K Jan 31 22:48 yahs_out_no_break.agp
-rw-r--r--    1 1001     118         4.2K Jan 31 22:48 yahs_out_scaffolds_final.agp
-rw-r--r--    1 1001     118         1.9M Jan 31 22:48 yahs_out_scaffolds_final.fa
lrwxrwxrwx    1 1001     118           77 Jan 31 22:48 ./input.bam -> /tmp/tmp72uiczf6/files/7/7/7/dataset_7770103d-bd3f-415c-93ef-0bcf1d84abfc.dat
lrwxrwxrwx    1 1001     118           77 Jan 31 22:48 ./input.fasta -> /tmp/tmp72uiczf6/files/e/f/7/dataset_ef772890-3dde-4adb-82b3-5f8615b5c2b8.dat
-rw-r--r--    1 1001     118         3.5K Jan 31 22:48 ./input.fasta.fai
-rw-r--r--    1 1001     118         5.1K Jan 31 22:48 ./output.log
-rw-r--r--    1 1001     118         5.6M Jan 31 22:48 ./yahs_out.bin

./agp_break:
total 16K    
drwxr-xr-x    2 1001     118         4.0K Jan 31 22:48 .
drwxr-xr-x    6 1001     118         4.0K Jan 31 22:48 ..
-rw-r--r--    1 1001     118         4.2K Jan 31 22:48 yahs_out_no_break.agp

./agp_out:
total 8K     
drwxr-xr-x    2 1001     118         4.0K Jan 31 22:48 .
drwxr-xr-x    6 1001     118         4.0K Jan 31 22:48 ..

./final_outs:
total 2M     
drwxr-xr-x    2 1001     118         4.0K Jan 31 22:48 .
drwxr-xr-x    6 1001     118         4.0K Jan 31 22:48 ..
-rw-r--r--    1 1001     118         4.2K Jan 31 22:48 yahs_out_scaffolds_final.agp
-rw-r--r--    1 1001     118         1.9M Jan 31 22:48 yahs_out_scaffolds_final.fa

./initial_break:
total 8K     
drwxr-xr-x    2 1001     118         4.0K Jan 31 22:48 .
drwxr-xr-x    6 1001     118         4.0K Jan 31 22:48 ..

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function	`{"__current_case__": 0, "agp": null, "bfile": {"values": [{"id": 18, "src": "hda"}]}, "enzyme_conditional": {"__current_case__": 1, "enzyme_options": "preconfigured", "preconfigured_enzymes": "arima2"}, "fasta": {"values": [{"id": 9, "src": "hda"}]}, "function_select": "yahs", "length": null, "no_contig_ec": true, "no_scaffold_ec": false, "quality": null, "res": ""}`
log_out	`true`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmp72uiczf6/files/a/e/e/dataset_aee0ee40-eeac-45e9-804c-b6230b7277b7.dat -f png -r 1000 -c 5 --sequences '=full' --minTexels 64 --gridSize 0 '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmp72uiczf6/files/a/e/e/dataset_aee0ee40-eeac-45e9-804c-b6230b7277b7.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 1000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 0 pixels
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 1, "showGrid": "no"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmp72uiczf6/job_working_directory/000/21/outputs/dataset_c0d0b893-b150-43ed-ae6b-8cd78fa67081.dat' -g  -w  -r 'scaffold_[0-9]*' '$&.hap1' '/tmp/tmp72uiczf6/files/b/a/b/dataset_bab9bdd7-7b1d-4294-af43-e338d8332580.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "scaffold_[0-9]*", "global": true, "is_regex": true, "replace_pattern": "$&.hap1", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": true}]`

Step 29: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
input	`{"values": [{"id": 12, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp72uiczf6/files/e/f/7/dataset_ef772890-3dde-4adb-82b3-5f8615b5c2b8.dat' --agp-to-path /tmp/tmp72uiczf6/files/c/0/d/dataset_c0d0b893-b150-43ed-ae6b-8cd78fa67081.dat  -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 83
Total scaffold length: 1971489
Average scaffold length: 23752.88
Scaffold N50: 20934
Scaffold auN: 34029.81
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11828
# contigs: 83
Total contig length: 1971489
Average contig length: 23752.88
Contig N50: 20934
Contig auN: 34029.81
Contig L50: 30
Largest contig: 132632
Smallest contig: 11828
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 603206:382062:383274:602947
GC content %: 38.82
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 83

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 2, "agp_to_path": {"values": [{"id": 23, "src": "hda"}]}, "discover_paths": false, "selector": "scaffolding"}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 4: Hi-C reverse reads:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp72uiczf6/files/d/5/6/dataset_d56e1cb2-cc86-4f4c-9aa6-d049b4f63491.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 83
Total scaffold length: 1971489
Average scaffold length: 23752.88
Scaffold N50: 20934
Scaffold auN: 34029.81
Scaffold L50: 30
Largest scaffold: 132632
Smallest scaffold: 11828
# contigs: 83
Total contig length: 1971489
Average contig length: 23752.88
Contig N50: 20934
Contig auN: 34029.81
Contig L50: 30
Largest contig: 132632
Smallest contig: 11828
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 603206:382062:383274:602947
GC content %: 38.82
# soft-masked bases: 0
# segments: 84
Total segment length: 1982895
Average segment length: 23605.89
# gaps: 0
# paths: 83

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp72uiczf6/files/d/5/6/dataset_d56e1cb2-cc86-4f4c-9aa6-d049b4f63491.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmp72uiczf6/job_working_directory/000/24/outputs/dataset_0d39518b-e84e-4c5b-b790-310fbb881ffe.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 33: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp72uiczf6/files/d/5/6/dataset_d56e1cb2-cc86-4f4c-9aa6-d049b4f63491.dat' --out-size s   --tabular > '/tmp/tmp72uiczf6/job_working_directory/000/25/outputs/dataset_0d343178-dfd6-4fd6-ad82-7c84d0d8ffd0.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "s", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 34: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp72uiczf6/files/1/9/e/dataset_19eb3a22-6f24-4740-8366-6f4a00e224e2.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmp72uiczf6/files/a/7/6/dataset_a76a5328-6850-4fa9-86a6-90691dc1c7bb.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp72uiczf6/job_working_directory/000/26/outputs/dataset_81114c4d-c00d-453d-8737-1f77be1b6125.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 161145786
ref seq len = 3942978
binary seq ticks = 83280767
build suffix-array ticks = 742057690
pos: 492873, ref_seq_len__: 492872
build fm-index ticks = 214292557
Total time taken: 0.5107
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3942979
* sentinel-index: 3258568
* Count:
0,	1
1,	1206154
2,	1971490
3,	2736826
4,	3942979

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3942978 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000037, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000037 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000053, nseq: 100108
	[0000][ M::kt_pipeline] read 100108 sequences (10000053 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 6.685 CPU sec, 7.099 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000072, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000072 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100108 reads in 6.763 CPU sec, 7.199 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000203, nseq: 100132
	[0000][ M::kt_pipeline] read 100132 sequences (10000203 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 6.637 CPU sec, 7.130 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000073, nseq: 100186
	[0000][ M::kt_pipeline] read 100186 sequences (10000073 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100132 reads in 6.697 CPU sec, 7.069 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000141, nseq: 100166
	[0000][ M::kt_pipeline] read 100166 sequences (10000141 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100186 reads in 6.805 CPU sec, 7.685 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000104, nseq: 118598
	[0000][ M::kt_pipeline] read 118598 sequences (10000104 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100166 reads in 6.759 CPU sec, 7.411 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000109, nseq: 151884
	[0000][ M::kt_pipeline] read 151884 sequences (10000109 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118598 reads in 6.695 CPU sec, 8.022 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000126, nseq: 151908
	[0000][ M::kt_pipeline] read 151908 sequences (10000126 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151884 reads in 6.157 CPU sec, 7.428 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151908 reads in 5.993 CPU sec, 7.156 real sec
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000007, nseq: 151868
	[0000][ M::kt_pipeline] read 151868 sequences (10000007 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 5.949 CPU sec, 6.980 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000077, nseq: 151870
	[0000][ M::kt_pipeline] read 151870 sequences (10000077 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151868 reads in 5.998 CPU sec, 7.069 real sec
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000024, nseq: 127818
	[0000][ M::kt_pipeline] read 127818 sequences (10000024 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151870 reads in 5.914 CPU sec, 7.044 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000071, nseq: 98956
	[0000][ M::kt_pipeline] read 98956 sequences (10000071 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127818 reads in 8.159 CPU sec, 9.690 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000004, nseq: 145156
	[0000][ M::kt_pipeline] read 145156 sequences (10000004 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98956 reads in 9.741 CPU sec, 9.937 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3496096, nseq: 53016
	[0000][ M::kt_pipeline] read 53016 sequences (3496096 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145156 reads in 8.826 CPU sec, 8.969 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 53016 reads in 2.586 CPU sec, 2.679 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.616827 MHz
Runtime profile:

	Time taken for main_mem function: 118.84 sec

	IO times (sec) :
	Reading IO time (reads) avg: 5.81, (5.81, 5.81)
	Writing IO time (SAM) avg: 4.90, (4.90, 4.90)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 118.83
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 118.56, (118.56, 118.56)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 11.30, (11.30, 11.30)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 107.26, (107.26, 107.26)
		SMEM compute avg: 34.15, (34.15, 34.15)
		SAL compute avg: 21.33, (21.33, 21.33)
				MEM_SA avg: 10.75, (10.75, 10.75)

		BSW time, avg: 44.95, (44.95, 44.95)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3942978
count = 0, 1206153, 1971489, 2736825, 3942978
BWT[3258568] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61609

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 14, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 25, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp72uiczf6/files/1/9/e/dataset_19eb3a22-6f24-4740-8366-6f4a00e224e2.dat' 'localref.fa' && bwa-mem2 index 'localref.fa' &&    bwa-mem2 mem -t "${GALAXY_SLOTS:-1}" -v 1                'localref.fa' '/tmp/tmp72uiczf6/files/8/4/4/dataset_844a71fb-161e-4be5-8bd0-23d749182684.dat'  | samtools sort -n -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp72uiczf6/job_working_directory/000/27/outputs/dataset_2f9fe842-4f5d-4abe-82f4-565048ee5b10.dat'

Exit Code:

```
0
```

Standard Error:

Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
[bwa_index] Pack FASTA... 0.01 sec
* Entering FMI_search
init ticks = 154884757
ref seq len = 3942978
binary seq ticks = 86198717
build suffix-array ticks = 775889520
pos: 492873, ref_seq_len__: 492872
build fm-index ticks = 215485168
Total time taken: 0.5194
Looking to launch executable "/usr/local/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/usr/local/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: localref.fa
* Entering FMI_search
* Index file found. Loading index from localref.fa.bwt.2bit.64
* Reference seq len for bi-index = 3942979
* sentinel-index: 3258568
* Count:
0,	1
1,	1206154
2,	1971490
3,	2736826
4,	3942979

* Reading other elements of the index from files localref.fa
* Index prefix: localref.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = localref.fa.0123
* Reference genome size: 3942978 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 139.3584 MB
2. Memory pre-allocation for BSW: 239.6170 MB
3. Memory pre-allocation for BWT: 77.3142 MB
------------------------------------------
* Threads used (compute): 1
* No. of pipeline threads: 2

[0000] read_chunk: 10000000, work_chunk_size: 10000036, nseq: 100212
	[0000][ M::kt_pipeline] read 100212 sequences (10000036 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000140, nseq: 100074
	[0000][ M::kt_pipeline] read 100074 sequences (10000140 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100212 reads in 6.722 CPU sec, 7.164 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000066, nseq: 100106
	[0000][ M::kt_pipeline] read 100106 sequences (10000066 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100074 reads in 6.651 CPU sec, 7.121 real sec
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000070, nseq: 100180
	[0000][ M::kt_pipeline] read 100180 sequences (10000070 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100106 reads in 6.864 CPU sec, 7.369 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000000, nseq: 100202
	[0000][ M::kt_pipeline] read 100202 sequences (10000000 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100180 reads in 6.342 CPU sec, 6.813 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000132, nseq: 100150
	[0000][ M::kt_pipeline] read 100150 sequences (10000132 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100202 reads in 6.575 CPU sec, 6.963 real sec
[0000] Calling mem_process_seqs.., task: 5
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000083, nseq: 118588
	[0000][ M::kt_pipeline] read 118588 sequences (10000083 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 100150 reads in 6.564 CPU sec, 7.087 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 6
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000125, nseq: 151900
	[0000][ M::kt_pipeline] read 151900 sequences (10000125 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 118588 reads in 6.699 CPU sec, 7.552 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 7
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000005, nseq: 151874
	[0000][ M::kt_pipeline] read 151874 sequences (10000005 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151900 reads in 6.276 CPU sec, 7.115 real sec
[0000] Calling mem_process_seqs.., task: 8
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151904
	[0000][ M::kt_pipeline] read 151904 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151874 reads in 6.311 CPU sec, 7.048 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 9
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 151896
	[0000][ M::kt_pipeline] read 151896 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151904 reads in 6.165 CPU sec, 7.638 real sec
[0000] Calling mem_process_seqs.., task: 10
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000130, nseq: 151906
	[0000][ M::kt_pipeline] read 151906 sequences (10000130 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151896 reads in 6.049 CPU sec, 7.265 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 11
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000100, nseq: 127808
	[0000][ M::kt_pipeline] read 127808 sequences (10000100 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 151906 reads in 6.051 CPU sec, 7.473 real sec
[0000] Calling mem_process_seqs.., task: 12
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000028, nseq: 98948
	[0000][ M::kt_pipeline] read 98948 sequences (10000028 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 127808 reads in 8.187 CPU sec, 9.797 real sec
[0000] Calling mem_process_seqs.., task: 13
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 10000026, nseq: 145218
	[0000][ M::kt_pipeline] read 145218 sequences (10000026 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 98948 reads in 11.000 CPU sec, 12.812 real sec
[0000] Calling mem_process_seqs.., task: 14
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 3489223, nseq: 52906
	[0000][ M::kt_pipeline] read 52906 sequences (3489223 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 145218 reads in 8.260 CPU sec, 8.438 real sec
[0000] Calling mem_process_seqs.., task: 15
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] 3. Calling kt_for - worker_sam
	[0000][ M::mem_process_seqs] Processed 52906 reads in 3.085 CPU sec, 3.255 real sec
[0000] read_chunk: 10000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 1
Processor is running @2445.602201 MHz
Runtime profile:

	Time taken for main_mem function: 121.27 sec

	IO times (sec) :
	Reading IO time (reads) avg: 6.45, (6.45, 6.45)
	Writing IO time (SAM) avg: 5.30, (5.30, 5.30)
	Reading IO time (Reference Genome) avg: 0.00, (0.00, 0.00)
	Index read time avg: 0.01, (0.01, 0.01)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 121.26
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 120.90, (120.90, 120.90)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 11.08, (11.08, 11.08)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 109.83, (109.83, 109.83)
		SMEM compute avg: 35.21, (35.21, 35.21)
		SAL compute avg: 21.80, (21.80, 21.80)
				MEM_SA avg: 10.97, (10.97, 10.97)

		BSW time, avg: 46.01, (46.01, 46.01)

Important parameter settings: 
	BATCH_SIZE: 512
	MAX_SEQ_LEN_REF: 256
	MAX_SEQ_LEN_QER: 128
	MAX_SEQ_LEN8: 128
	SEEDS_PER_READ: 500
	SIMD_WIDTH8 X: 32
	SIMD_WIDTH16 X: 16
	AVG_SEEDS_PER_READ: 64

Standard Output:

ref_seq_len = 3942978
count = 0, 1206153, 1971489, 2736825, 3942978
BWT[3258568] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
max_occ_ind = 61609

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 1, "fastq_input1": {"values": [{"id": 15, "src": "hda"}]}, "fastq_input_selector": "single"}`
output_sort	`"name"`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 25, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 36: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp72uiczf6/files/1/9/e/dataset_19eb3a22-6f24-4740-8366-6f4a00e224e2.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'vertebrata_odb10'  --metaeuk  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific

Exit Code:

```
0
```

Standard Error:

2025-01-31 23:54:45 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2025-01-31 22:50:39 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 01/31/2025 22:50:39 *****
2025-01-31 22:50:39 INFO:	Configuring BUSCO with local environment
2025-01-31 22:50:39 INFO:	Running genome mode
2025-01-31 22:57:04 INFO:	Input file is /tmp/tmp72uiczf6/files/1/9/e/dataset_19eb3a22-6f24-4740-8366-6f4a00e224e2.dat
2025-01-31 22:57:04 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2025-01-31 22:57:04 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_met
2025-01-31 22:57:04 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2025-01-31 22:57:04 INFO:	Running 1 job(s) on bbtools, starting at 01/31/2025 22:57:04
2025-01-31 22:57:05 INFO:	[bbtools]	1 of 1 task(s) completed
2025-01-31 22:57:05 INFO:	Running 1 job(s) on metaeuk, starting at 01/31/2025 22:57:05
2025-01-31 23:27:36 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-01-31 23:27:36 INFO:	***** Run HMMER on gene sequences *****
2025-01-31 23:27:37 INFO:	Running 3354 job(s) on hmmsearch, starting at 01/31/2025 23:27:37
2025-01-31 23:29:39 INFO:	[hmmsearch]	336 of 3354 task(s) completed
2025-01-31 23:31:35 INFO:	[hmmsearch]	671 of 3354 task(s) completed
2025-01-31 23:33:20 INFO:	[hmmsearch]	1007 of 3354 task(s) completed
2025-01-31 23:35:17 INFO:	[hmmsearch]	1342 of 3354 task(s) completed
2025-01-31 23:36:57 INFO:	[hmmsearch]	1677 of 3354 task(s) completed
2025-01-31 23:38:22 INFO:	[hmmsearch]	2013 of 3354 task(s) completed
2025-01-31 23:39:40 INFO:	[hmmsearch]	2348 of 3354 task(s) completed
2025-01-31 23:40:57 INFO:	[hmmsearch]	2684 of 3354 task(s) completed
2025-01-31 23:42:31 INFO:	[hmmsearch]	3019 of 3354 task(s) completed
2025-01-31 23:44:41 INFO:	[hmmsearch]	3354 of 3354 task(s) completed
2025-01-31 23:44:42 INFO:	54 exons in total
2025-01-31 23:44:42 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2025-01-31 23:46:29 INFO:	Running 1 job(s) on metaeuk, starting at 01/31/2025 23:46:29
2025-01-31 23:54:07 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-01-31 23:54:07 INFO:	***** Run HMMER on gene sequences *****
2025-01-31 23:54:07 INFO:	Running 3318 job(s) on hmmsearch, starting at 01/31/2025 23:54:07
2025-01-31 23:54:11 INFO:	[hmmsearch]	332 of 3318 task(s) completed
2025-01-31 23:54:14 INFO:	[hmmsearch]	664 of 3318 task(s) completed
2025-01-31 23:54:18 INFO:	[hmmsearch]	996 of 3318 task(s) completed
2025-01-31 23:54:21 INFO:	[hmmsearch]	1328 of 3318 task(s) completed
2025-01-31 23:54:24 INFO:	[hmmsearch]	1660 of 3318 task(s) completed
2025-01-31 23:54:28 INFO:	[hmmsearch]	1991 of 3318 task(s) completed
2025-01-31 23:54:31 INFO:	[hmmsearch]	2323 of 3318 task(s) completed
2025-01-31 23:54:35 INFO:	[hmmsearch]	2655 of 3318 task(s) completed
2025-01-31 23:54:38 INFO:	[hmmsearch]	2987 of 3318 task(s) completed
2025-01-31 23:54:41 INFO:	[hmmsearch]	3318 of 3318 task(s) completed
2025-01-31 23:54:42 INFO:	5 candidate overlapping regions found
2025-01-31 23:54:42 INFO:	62 exons in total
2025-01-31 23:54:42 INFO:	Results:	C:1.1%[S:1.0%,D:0.0%],F:0.4%,M:98.5%,n:3354	   

2025-01-31 23:54:42 INFO:	

    ---------------------------------------------------
    |Results from dataset vertebrata_odb10             |
    ---------------------------------------------------
    |C:1.1%[S:1.0%,D:0.0%],F:0.4%,M:98.5%,n:3354       |
    |36    Complete BUSCOs (C)                         |
    |35    Complete and single-copy BUSCOs (S)         |
    |1    Complete and duplicated BUSCOs (D)           |
    |15    Fragmented BUSCOs (F)                       |
    |3303    Missing BUSCOs (M)                        |
    |3354    Total BUSCO groups searched               |
    ---------------------------------------------------
2025-01-31 23:54:42 INFO:	BUSCO analysis done with WARNING(s). Total running time: 3458 seconds

***** Summary of warnings: *****
2025-01-31 22:57:04 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2025-01-31 22:57:04 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_genome_met

2025-01-31 23:54:42 INFO:	Results written in /tmp/tmp72uiczf6/job_working_directory/000/28/working/busco_galaxy
2025-01-31 23:54:42 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-01-31 23:54:42 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 140
drwxr-xr-x 5 1001 118  4096 Jan 31 22:57 busco_sequences
-rw-r--r-- 1 1001 118 76396 Jan 31 23:54 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Jan 31 23:44 hmmer_output
drwxr-xr-x 4 1001 118  4096 Jan 31 23:54 metaeuk_output
-rw-r--r-- 1 1001 118 42380 Jan 31 23:54 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2953 Jan 31 23:54 short_summary.json
-rw-r--r-- 1 1001 118   969 Jan 31 23:54 short_summary.txt
2025-01-31 23:54:43 INFO:	****************** Start plot generation at 01/31/2025 23:54:43 ******************
2025-01-31 23:54:43 INFO:	Load data ...
2025-01-31 23:54:43 INFO:	Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2025-01-31 23:54:43 INFO:	Generate the R code ...
2025-01-31 23:54:43 INFO:	Run the R code ...
2025-01-31 23:54:45 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-01-31 23:54:45 INFO:	Plot generation done. Total running time: 2.140200138092041 seconds
2025-01-31 23:54:45 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "metaeuk"}}`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image"]`

Step 37: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmp72uiczf6/job_working_directory/000/29/outputs/dataset_46c73a8f-3f29-4dc1-81f5-f85079896dd4.dat' -g     '#' 'Number of' '/tmp/tmp72uiczf6/files/0/d/3/dataset_0d39518b-e84e-4c5b-b790-310fbb881ffe.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 38: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp72uiczf6/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmp72uiczf6/files/0/d/3/dataset_0d343178-dfd6-4fd6-ad82-7c84d0d8ffd0.dat' --output='/tmp/tmp72uiczf6/job_working_directory/000/30/outputs/dataset_d383b7a1-f4fb-4685-9a63-4abae97b6f62.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"ddcd6b2be02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp72uiczf6/job_working_directory/000/31/configs/tmpelycxjlk' '/tmp/tmp72uiczf6/files/d/3/8/dataset_d383b7a1-f4fb-4685-9a63-4abae97b6f62.dat' > '/tmp/tmp72uiczf6/job_working_directory/000/31/outputs/dataset_1085091a-bf19-4305-92eb-59c33b5afba9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2be02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmp72uiczf6/files/1/0/8/dataset_1085091a-bf19-4305-92eb-59c33b5afba9.dat > '/tmp/tmp72uiczf6/job_working_directory/000/32/outputs/dataset_1868b1bd-fd48-4faf-bed7-c5adad868a5d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2be02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp72uiczf6/files/1/0/8/dataset_1085091a-bf19-4305-92eb-59c33b5afba9.dat" "/tmp/tmp72uiczf6/job_working_directory/000/33/outputs/dataset_cfbed787-426e-4c3d-a47d-81d1a8141827.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2be02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"ddcd6b2be02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2be02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1971489", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmp72uiczf6/job_working_directory/000/42/configs/tmp6r21hwgp' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp72uiczf6/files/c/f/b/dataset_cfbed787-426e-4c3d-a47d-81d1a8141827.dat' '/tmp/tmp72uiczf6/job_working_directory/000/42/outputs/dataset_8bc3e236-305e-45e1-b75c-d0b91457997a.dat'

Exit Code:

```
0
```

Standard Output:

c3/1971489
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1971489;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 83 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2be02411efb9ab7c1e523ef409"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1971489"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 39: toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp72uiczf6/files/8/1/1/dataset_81114c4d-c00d-453d-8737-1f77be1b6125.dat' 'forward_input.bam' && ln -s '/tmp/tmp72uiczf6/files/2/f/9/dataset_2f9fe842-4f5d-4abe-82f4-565048ee5b10.dat' 'reverse_input.bam' && bellerophon --forward forward_input.bam --reverse reverse_input.bam --quality 20 --output 'merged_out.bam' --threads ${GALAXY_SLOTS:-1} && samtools sort --no-PG -O BAM -o '/tmp/tmp72uiczf6/job_working_directory/000/35/outputs/dataset_b410a4d9-dec1-4928-ba68-91727c718581.dat' -@ ${GALAXY_SLOTS:-1} merged_out.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
quality	`"20"`

Step 40: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp72uiczf6/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp72uiczf6/files/8/b/c/dataset_8bc3e236-305e-45e1-b75c-d0b91457997a.dat' 'c5,c6' T '/tmp/tmp72uiczf6/job_working_directory/000/43/outputs/dataset_8c8d41de-cdfb-44fc-81a8-a6a985f348a1.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 5: Trim Hi-C Data?:
- step_state: scheduled

Step 41: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp72uiczf6/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp72uiczf6/files/8/b/c/dataset_8bc3e236-305e-45e1-b75c-d0b91457997a.dat' 'c4,c7' T '/tmp/tmp72uiczf6/job_working_directory/000/44/outputs/dataset_305b8f21-56f5-48f6-8c97-c9c55d9a70ea.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 42: toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

samtools view -h '/tmp/tmp72uiczf6/files/b/4/1/dataset_b410a4d9-dec1-4928-ba68-91727c718581.dat' | PretextMap -o output.pretext

Exit Code:

```
0
```

Standard Output:

[PretextMap status] :: Mapping to 83 sequences, sorted by length, descending. Filtering by minimum mapping quality 10

                                                                                
[PretextMap status] :: 10.0 k reads processed, 5.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 20.0 k reads processed, 10.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 30.0 k reads processed, 15.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 40.0 k reads processed, 20.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 50.0 k reads processed, 25.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 60.0 k reads processed, 30.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 70.0 k reads processed, 35.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 80.0 k reads processed, 40.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 90.0 k reads processed, 45.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 100.0 k reads processed, 50.1 k read-pairs mapped
                                                                                
[PretextMap status] :: 110.0 k reads processed, 55.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 120.0 k reads processed, 60.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 130.0 k reads processed, 65.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 140.0 k reads processed, 70.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 150.0 k reads processed, 75.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 160.0 k reads processed, 80.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 170.0 k reads processed, 85.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 180.0 k reads processed, 90.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 190.0 k reads processed, 95.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 200.0 k reads processed, 100.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 210.0 k reads processed, 105.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 220.0 k reads processed, 109.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 230.0 k reads processed, 114.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 240.0 k reads processed, 119.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 250.0 k reads processed, 125.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 260.0 k reads processed, 130.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 270.0 k reads processed, 135.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 280.0 k reads processed, 139.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 290.0 k reads processed, 144.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 300.0 k reads processed, 149.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 310.0 k reads processed, 154.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 320.0 k reads processed, 159.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 330.0 k reads processed, 164.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 340.0 k reads processed, 169.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 350.0 k reads processed, 174.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 360.0 k reads processed, 179.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 370.0 k reads processed, 184.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 380.0 k reads processed, 190.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 390.0 k reads processed, 195.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 400.0 k reads processed, 199.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 410.0 k reads processed, 204.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 420.0 k reads processed, 209.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 430.0 k reads processed, 214.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 440.0 k reads processed, 219.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 450.0 k reads processed, 224.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 460.0 k reads processed, 229.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 470.0 k reads processed, 234.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 480.0 k reads processed, 239.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 490.0 k reads processed, 245.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 500.0 k reads processed, 250.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 510.0 k reads processed, 255.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 520.0 k reads processed, 260.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 530.0 k reads processed, 265.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 540.0 k reads processed, 270.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 550.0 k reads processed, 275.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 560.0 k reads processed, 280.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 570.0 k reads processed, 285.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 580.0 k reads processed, 290.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 590.0 k reads processed, 294.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 600.0 k reads processed, 300.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 610.0 k reads processed, 305.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 620.0 k reads processed, 310.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 630.0 k reads processed, 314.9 k read-pairs mapped
                                                                                
[PretextMap status] :: 640.0 k reads processed, 320.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 650.0 k reads processed, 325.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 660.0 k reads processed, 330.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 670.0 k reads processed, 335.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 680.0 k reads processed, 340.0 k read-pairs mapped
                                                                                
[PretextMap status] :: 690.0 k reads processed, 345.0 k read-pairs mapped
[PretextMap status] :: Creating MipMaps...
[PretextMap status] :: Equalising contrast...
[PretextMap status] :: Compressing textures...

[PretextMap status] ::   1/528 (0.19%) texture blocks written to disk
[PretextMap status] ::   2/528 (0.38%) texture blocks written to disk
[PretextMap status] ::   3/528 (0.57%) texture blocks written to disk
[PretextMap status] ::   4/528 (0.76%) texture blocks written to disk
[PretextMap status] ::   5/528 (0.95%) texture blocks written to disk
[PretextMap status] ::   6/528 (1.14%) texture blocks written to disk
[PretextMap status] ::   7/528 (1.33%) texture blocks written to disk
[PretextMap status] ::   8/528 (1.52%) texture blocks written to disk
[PretextMap status] ::   9/528 (1.70%) texture blocks written to disk
[PretextMap status] ::  10/528 (1.89%) texture blocks written to disk
[PretextMap status] ::  11/528 (2.08%) texture blocks written to disk
[PretextMap status] ::  12/528 (2.27%) texture blocks written to disk
[PretextMap status] ::  13/528 (2.46%) texture blocks written to disk
[PretextMap status] ::  14/528 (2.65%) texture blocks written to disk
[PretextMap status] ::  15/528 (2.84%) texture blocks written to disk
[PretextMap status] ::  16/528 (3.03%) texture blocks written to disk
[PretextMap status] ::  17/528 (3.22%) texture blocks written to disk
[PretextMap status] ::  18/528 (3.41%) texture blocks written to disk
[PretextMap status] ::  19/528 (3.60%) texture blocks written to disk
[PretextMap status] ::  20/528 (3.79%) texture blocks written to disk
[PretextMap status] ::  21/528 (3.98%) texture blocks written to disk
[PretextMap status] ::  22/528 (4.17%) texture blocks written to disk
[PretextMap status] ::  23/528 (4.36%) texture blocks written to disk
[PretextMap status] ::  24/528 (4.55%) texture blocks written to disk
[PretextMap status] ::  25/528 (4.73%) texture blocks written to disk
[PretextMap status] ::  26/528 (4.92%) texture blocks written to disk
[PretextMap status] ::  27/528 (5.11%) texture blocks written to disk
[PretextMap status] ::  28/528 (5.30%) texture blocks written to disk
[PretextMap status] ::  29/528 (5.49%) texture blocks written to disk
[PretextMap status] ::  30/528 (5.68%) texture blocks written to disk
[PretextMap status] ::  31/528 (5.87%) texture blocks written to disk
[PretextMap status] ::  32/528 (6.06%) texture blocks written to disk
[PretextMap status] ::  33/528 (6.25%) texture blocks written to disk
[PretextMap status] ::  34/528 (6.44%) texture blocks written to disk
[PretextMap status] ::  35/528 (6.63%) texture blocks written to disk
[PretextMap status] ::  36/528 (6.82%) texture blocks written to disk
[PretextMap status] ::  37/528 (7.01%) texture blocks written to disk
[PretextMap status] ::  38/528 (7.20%) texture blocks written to disk
[PretextMap status] ::  39/528 (7.39%) texture blocks written to disk
[PretextMap status] ::  40/528 (7.58%) texture blocks written to disk
[PretextMap status] ::  41/528 (7.77%) texture blocks written to disk
[PretextMap status] ::  42/528 (7.95%) texture blocks written to disk
[PretextMap status] ::  43/528 (8.14%) texture blocks written to disk
[PretextMap status] ::  44/528 (8.33%) texture blocks written to disk
[PretextMap status] ::  45/528 (8.52%) texture blocks written to disk
[PretextMap status] ::  46/528 (8.71%) texture blocks written to disk
[PretextMap status] ::  47/528 (8.90%) texture blocks written to disk
[PretextMap status] ::  48/528 (9.09%) texture blocks written to disk
[PretextMap status] ::  49/528 (9.28%) texture blocks written to disk
[PretextMap status] ::  50/528 (9.47%) texture blocks written to disk
[PretextMap status] ::  51/528 (9.66%) texture blocks written to disk
[PretextMap status] ::  52/528 (9.85%) texture blocks written to disk
[PretextMap status] ::  53/528 (10.04%) texture blocks written to disk
[PretextMap status] ::  54/528 (10.23%) texture blocks written to disk
[PretextMap status] ::  55/528 (10.42%) texture blocks written to disk
[PretextMap status] ::  56/528 (10.61%) texture blocks written to disk
[PretextMap status] ::  57/528 (10.80%) texture blocks written to disk
[PretextMap status] ::  58/528 (10.98%) texture blocks written to disk
[PretextMap status] ::  59/528 (11.17%) texture blocks written to disk
[PretextMap status] ::  60/528 (11.36%) texture blocks written to disk
[PretextMap status] ::  61/528 (11.55%) texture blocks written to disk
[PretextMap status] ::  62/528 (11.74%) texture blocks written to disk
[PretextMap status] ::  63/528 (11.93%) texture blocks written to disk
[PretextMap status] ::  64/528 (12.12%) texture blocks written to disk
[PretextMap status] ::  65/528 (12.31%) texture blocks written to disk
[PretextMap status] ::  66/528 (12.50%) texture blocks written to disk
[PretextMap status] ::  67/528 (12.69%) texture blocks written to disk
[PretextMap status] ::  68/528 (12.88%) texture blocks written to disk
[PretextMap status] ::  69/528 (13.07%) texture blocks written to disk
[PretextMap status] ::  70/528 (13.26%) texture blocks written to disk
[PretextMap status] ::  71/528 (13.45%) texture blocks written to disk
[PretextMap status] ::  72/528 (13.64%) texture blocks written to disk
[PretextMap status] ::  73/528 (13.83%) texture blocks written to disk
[PretextMap status] ::  74/528 (14.02%) texture blocks written to disk
[PretextMap status] ::  75/528 (14.20%) texture blocks written to disk
[PretextMap status] ::  76/528 (14.39%) texture blocks written to disk
[PretextMap status] ::  77/528 (14.58%) texture blocks written to disk
[PretextMap status] ::  78/528 (14.77%) textu
..
:: 298/528 (56.44%) texture blocks written to disk
[PretextMap status] :: 299/528 (56.63%) texture blocks written to disk
[PretextMap status] :: 300/528 (56.82%) texture blocks written to disk
[PretextMap status] :: 301/528 (57.01%) texture blocks written to disk
[PretextMap status] :: 302/528 (57.20%) texture blocks written to disk
[PretextMap status] :: 303/528 (57.39%) texture blocks written to disk
[PretextMap status] :: 304/528 (57.58%) texture blocks written to disk
[PretextMap status] :: 305/528 (57.77%) texture blocks written to disk
[PretextMap status] :: 306/528 (57.95%) texture blocks written to disk
[PretextMap status] :: 307/528 (58.14%) texture blocks written to disk
[PretextMap status] :: 308/528 (58.33%) texture blocks written to disk
[PretextMap status] :: 309/528 (58.52%) texture blocks written to disk
[PretextMap status] :: 310/528 (58.71%) texture blocks written to disk
[PretextMap status] :: 311/528 (58.90%) texture blocks written to disk
[PretextMap status] :: 312/528 (59.09%) texture blocks written to disk
[PretextMap status] :: 313/528 (59.28%) texture blocks written to disk
[PretextMap status] :: 314/528 (59.47%) texture blocks written to disk
[PretextMap status] :: 315/528 (59.66%) texture blocks written to disk
[PretextMap status] :: 316/528 (59.85%) texture blocks written to disk
[PretextMap status] :: 317/528 (60.04%) texture blocks written to disk
[PretextMap status] :: 318/528 (60.23%) texture blocks written to disk
[PretextMap status] :: 319/528 (60.42%) texture blocks written to disk
[PretextMap status] :: 320/528 (60.61%) texture blocks written to disk
[PretextMap status] :: 321/528 (60.80%) texture blocks written to disk
[PretextMap status] :: 322/528 (60.98%) texture blocks written to disk
[PretextMap status] :: 323/528 (61.17%) texture blocks written to disk
[PretextMap status] :: 324/528 (61.36%) texture blocks written to disk
[PretextMap status] :: 325/528 (61.55%) texture blocks written to disk
[PretextMap status] :: 326/528 (61.74%) texture blocks written to disk
[PretextMap status] :: 327/528 (61.93%) texture blocks written to disk
[PretextMap status] :: 328/528 (62.12%) texture blocks written to disk
[PretextMap status] :: 329/528 (62.31%) texture blocks written to disk
[PretextMap status] :: 330/528 (62.50%) texture blocks written to disk
[PretextMap status] :: 331/528 (62.69%) texture blocks written to disk
[PretextMap status] :: 332/528 (62.88%) texture blocks written to disk
[PretextMap status] :: 333/528 (63.07%) texture blocks written to disk
[PretextMap status] :: 334/528 (63.26%) texture blocks written to disk
[PretextMap status] :: 335/528 (63.45%) texture blocks written to disk
[PretextMap status] :: 336/528 (63.64%) texture blocks written to disk
[PretextMap status] :: 337/528 (63.83%) texture blocks written to disk
[PretextMap status] :: 338/528 (64.02%) texture blocks written to disk
[PretextMap status] :: 339/528 (64.20%) texture blocks written to disk
[PretextMap status] :: 340/528 (64.39%) texture blocks written to disk
[PretextMap status] :: 341/528 (64.58%) texture blocks written to disk
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[PretextMap status] :: 344/528 (65.15%) texture blocks written to disk
[PretextMap status] :: 345/528 (65.34%) texture blocks written to disk
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[PretextMap status] :: 348/528 (65.91%) texture blocks written to disk
[PretextMap status] :: 349/528 (66.10%) texture blocks written to disk
[PretextMap status] :: 350/528 (66.29%) texture blocks written to disk
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[PretextMap status] :: 352/528 (66.67%) texture blocks written to disk
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[PretextMap status] :: 354/528 (67.05%) texture blocks written to disk
[PretextMap status] :: 355/528 (67.23%) texture blocks written to disk
[PretextMap status] :: 356/528 (67.42%) texture blocks written to disk
[PretextMap status] :: 357/528 (67.61%) texture blocks written to disk
[PretextMap status] :: 358/528 (67.80%) texture blocks written to disk
[PretextMap status] :: 359/528 (67.99%) texture blocks written to disk
[PretextMap status] :: 360/528 (68.18%) texture blocks written to disk
[PretextMap status] :: 361/528 (68.37%) texture blocks written to disk
[PretextMap status] :: 362/528 (68.56%) texture blocks written to disk
[PretextMap status] :: 363/528 (68.75%) texture blocks written to disk
[PretextMap status] :: 364/528 (68.94%) texture blocks written to disk
[PretextMap status] :: 365/528 (69.13%) texture blocks written to disk
[PretextMap status] :: 366/528 (69.32%) texture blocks written to disk
[PretextMap status] :: 367/528 (69.51%) texture blocks written to disk
[PretextMap status] :: 368/528 (69.70%) texture blocks written to disk
[PretextMap status] :: 369/528 (69.89%) texture blocks written to disk
[PretextMap status] :: 370/528 (70.08%) texture blocks written to disk
[PretextMap status] :: 371/528 (70.27%) texture blocks written to disk
[PretextMap status] :: 372/528 (70.45%) texture blocks written to disk
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[PretextMap status] :: 386/528 (73.11%) texture blocks written to disk
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[PretextMap status] :: 396/528 (75.00%) texture blocks written to disk
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[PretextMap status] :: 406/528 (76.89%) texture blocks written to disk
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[PretextMap status] :: 409/528 (77.46%) texture blocks written to disk
[PretextMap status] :: 410/528 (77.65%) texture blocks written to disk
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[PretextMap status] :: 412/528 (78.03%) texture blocks written to disk
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[PretextMap status] :: 415/528 (78.60%) texture blocks written to disk
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[PretextMap status] :: 418/528 (79.17%) texture blocks written to disk
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[PretextMap status] :: 425/528 (80.49%) texture blocks written to disk
[PretextMap status] :: 426/528 (80.68%) texture blocks written to disk
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[PretextMap status] :: 428/528 (81.06%) texture blocks written to disk
[PretextMap status] :: 429/528 (81.25%) texture blocks written to disk
[PretextMap status] :: 430/528 (81.44%) texture blocks written to disk
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Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter	`{"__current_case__": 0, "filter_type": ""}`
map_qual	`None`
sorting	`{"__current_case__": 0, "sortby": "nosort"}`

Step 43: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp72uiczf6/files/b/4/1/dataset_b410a4d9-dec1-4928-ba68-91727c718581.dat' ./input.bam &&  bedtools bamtobed -bed12   -i ./input.bam > '/tmp/tmp72uiczf6/job_working_directory/000/37/outputs/dataset_b92a4abc-f4b8-4c1a-a1cc-b62e05097d1f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ed_score	`false`
option	`"-bed12"`
split	`false`
tag	`""`

Step 44: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp72uiczf6/job_working_directory/000/45/configs/tmp0478j0_h' && Rscript '/tmp/tmp72uiczf6/job_working_directory/000/45/configs/tmp0478j0_h'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp72uiczf6/files/8/c/8/dataset_8c8d41de-cdfb-44fc-81a8-a6a985f348a1.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp72uiczf6/job_working_directory/000/45/outputs/dataset_64a9cf3e-eb5a-4be4-af7a-10ee4fea3fe3.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"x"`
xplot	`"1"`
ylab	`"Nx (Mb)"`
yplot	`"2"`

Step 45: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp72uiczf6/job_working_directory/000/46/configs/tmp4a0_tavs' && Rscript '/tmp/tmp72uiczf6/job_working_directory/000/46/configs/tmp4a0_tavs'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp72uiczf6/files/3/0/5/dataset_305b8f21-56f5-48f6-8c97-c9c55d9a70ea.dat', sep='\t', header=TRUE)

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = NULL
    color_scale = NULL

        gg_line = geom_line(size=1, alpha=1, gg_factor)


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp72uiczf6/job_working_directory/000/46/outputs/dataset_c4a47c58-7a15-42e7-9d5d-a94c3b48d51b.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 0, "factoring": "Default"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"1"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"2"`

Step 46: toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

PretextSnapshot -m /tmp/tmp72uiczf6/files/c/3/7/dataset_c37099d8-b554-4979-afb4-506870e121f7.dat -f png -r 1000 -c 5 --sequences '=full' --minTexels 64 --gridSize 1 --gridColour black '' -o output --prefix pretext_snapshot

Exit Code:

```
0
```

Standard Output:

[PretextSnapshot status] :: Input map: '/tmp/tmp72uiczf6/files/c/3/7/dataset_c37099d8-b554-4979-afb4-506870e121f7.dat'
[PretextSnapshot status] :: Output format: png
[PretextSnapshot status] :: Output resolution: 1000 pixels
[PretextSnapshot status] :: Colour map: Three Wave Blue-Green-Yellow
[PretextSnapshot status] :: Minimum texels per image: 64
[PretextSnapshot status] :: Grid size: 1 pixel
[PretextSnapshot status] :: Grid colour: 000000ff
[PretextSnapshot status] :: Output path: 'output/pretext_snapshot'
[PretextSnapshot status] :: Indexing file...
[PretextSnapshot status] :: File indexed
[PretextSnapshot status] :: 'output/pretext_snapshotFullMap.png' written to disk

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
colormap	`"5"`
dbkey	`"?"`
formats	`{"__current_case__": 0, "outformat": "png"}`
grid	`{"__current_case__": 0, "gridcolor": "black", "gridsize": "1", "showGrid": "yes"}`
mintexels	`"64"`
resolution	`"1000"`
sequencenames	`false`
sequences	`"=full"`

Step 47: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

( LC_ALL=C  sort   --stable -t '	'  -k '4,4'  ) < '/tmp/tmp72uiczf6/files/b/9/2/dataset_b92a4abc-f4b8-4c1a-a1cc-b62e05097d1f.dat' > '/tmp/tmp72uiczf6/job_working_directory/000/39/outputs/dataset_160a6cb2-2577-46ff-9a1b-6eea6a3f2647.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
chromInfo	`"/tmp/tmp72uiczf6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`"0"`
ignore_case	`false`
sortkeys	`[{"__index__": 0, "column": "4", "order": "", "style": ""}]`
unique	`false`

Step 48: __EXTRACT_DATASET__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"ddcd6b2ae02411efb9ab7c1e523ef409"`
input	`{"values": [{"id": 13, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 6: Database for Busco Lineage:
- step_state: scheduled
Step 7: Lineage:
- step_state: scheduled
Step 8: Restriction enzymes:
- step_state: scheduled
Step 9: Estimated genome size - Parameter File:
- step_state: scheduled
Step 10: SAK input file:
- step_state: scheduled

Other invocation details
- history_id
  - 06112e6096c9939f
- history_state
  - ok
- invocation_id
  - 06112e6096c9939f
- invocation_state
  - scheduled
- workflow_id
  - 68667882b73043c0

gxydevbot · 2025-02-03T04:44:07Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot changed the title ~~Updating workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 from 0.2.7 to 0.2.8~~ Updating workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 from 0.2.7 to 0.2.8 Sep 23, 2024

gxydevbot force-pushed the workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 branch from 4f38eac to eb62260 Compare September 23, 2024 14:04

gxydevbot force-pushed the workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 branch from eb62260 to 25959e7 Compare September 24, 2024 13:41

gxydevbot force-pushed the workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 branch from 25959e7 to d784d7d Compare October 14, 2024 04:33

Delphine-L added 11 commits December 13, 2024 16:10

correct input names

bbd96ee

use metaeuk for busco gene predictor

f4ca428

use metaeuk for busco gene predictor

7f3bb49

Correct tests to pass the inputs as collections instead of files

ec2123c

Add trimmed read collections as outputs and change busco gene predictor

8019975

Update tests

e824e02

Update README.md

615cea2

Rename inputs

92ed363

Hide some steps

d5c37d4

Change updates to the latest versions

e8caae4

update gfastats with text format fix

ef340de

mvdbeek force-pushed the workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 branch from 26b9974 to ef340de Compare December 13, 2024 15:11

update busco test

fcf835a

Delphine-L added 4 commits January 31, 2025 15:56

add input annotations

dc4d132

update release date

f940d7c

change version number

acc941f

Change version number

2d37568

Delphine-L requested a review from mvdbeek February 1, 2025 15:02

mvdbeek merged commit e15f141 into galaxyproject:main Feb 4, 2025
7 checks passed

Updating workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 from 0.2.7 to 0.2.8 #514

Updating workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 from 0.2.7 to 0.2.8 #514

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