Important! Template update for nf-core/tools v3.2.0 #261
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Test pipeline with STAR aligner and RSEM for quantification.Params: --aligner star_rsem
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.04.2
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [distraught_borg] DSL2 - revision: 85c9b75b8b
Downloading plugin [email protected]
WARN: Invalid config manifest attribute `contributors`
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m nf-core/rnaseq 3.19.0dev[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
[0;34minput : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv[0m
[0;34moutdir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/e9ed2c3496454a69937adc9eb340c688/output[0m
[1mReference genome options[0m
[0;34mfasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta[0m
[0;34mgtf : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes_with_empty_tid.gtf.gz[0m
[0;34mgff : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz[0m
[0;34mtranscript_fasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta[0m
[0;34madditional_fasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz[0m
[0;34mhisat2_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz[0m
[0;34mrsem_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz[0m
[0;34msalmon_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz[0m
[0;34mhisat2_build_memory : [0;32m3.GB[0m
[1mRead filtering options[0m
[0;34mbbsplit_fasta_list : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt[0m
[1mUMI options[0m
[0;34mumitools_bc_pattern : [0;32mNNNN[0m
[1mAlignment options[0m
[0;34maligner : [0;32mstar_rsem[0m
[0;34mpseudo_aligner : [0;32msalmon[0m
[1mProcess skipping options[0m
[0;34mskip_bbsplit : [0;32mfalse[0m
[1mInstitutional config options[0m
[0;34mconfig_profile_name : [0;32mTest profile[0m
[0;34mconfig_profile_description : [0;32mMinimal test dataset to check pipeline function[0m
[1mGeneric options[0m
[0;34mpipelines_testdata_base_path: [0;32ms3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/[0m
[0;34mtrace_report_suffix : [0;32m2025-01-29_15-40-27[0m
[1mCore Nextflow options[0m
[0;34mrunName : [0;32mdistraught_borg[0m
[0;34mcontainerEngine : [0;32mdocker[0m
[0;34mlaunchDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/e9ed2c3496454a69937adc9eb340c688[0m
[0;34mworkDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/e9ed2c3496454a69937adc9eb340c688/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/rnaseq/rnaseq[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest,docker[0m
[0;34mconfigFiles : [0;32m/home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/tests/nextflow.config[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* The pipeline
https://doi.org/10.5281/zenodo.1400710
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md
WARN: The following invalid input values have been detected:
* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Both '--gtf' and '--gff' parameters have been provided.
Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
'--transcript_fasta' parameter has been provided.
Make sure transcript names in this file match those in the GFF/GTF file.
Please see:
https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When using '--additional_fasta <FASTA_FILE>' the aligner index will not
be re-built with the transgenes incorporated by default since you have
already provided an index via '--rsem_index <INDEX>'.
Set '--additional_fasta <FASTA_FILE> --rsem_index false --gene_bed false --save_reference'
to re-build the index with transgenes included and the index and gene BED file will be saved in
'results/genome/index/rsem/' for re-use with '--rsem_index'.
Ignore this warning if you know that the index already contains transgenes.
Please see:
https://github.com/nf-core/rnaseq/issues/556
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[bb/b6be2f] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[37/68d9ce] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[9b/490197] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[ee/272097] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[d6/11e477] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[7e/7474f1] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_IAA_30M_REP1)
[01/bb3e58] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP2)
[71/b8e639] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[97/891519] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
[61/836fa3] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[21/2d5bc7] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[1c/0d5829] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[40/bea280] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[cb/822fe5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[ef/143fbd] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_RSEM_INDEX (rsem.tar.gz)
[55/afadf6] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[e0/2d209e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[6c/40363c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[d7/bc5254] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP2)
[23/0ea3a5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_REP2)
[f5/3850ee] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_IAA_30M_REP1)
[a6/ebdefc] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP1)
[5d/02b500] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[e0/7aca24] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[c2/4468bd] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_UNINDUCED_REP1)
[13/c08d73] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[7f/52ce52] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_UNINDUCED_REP2)
[ce/5d8473] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[a5/c2a645] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[cd/97e131] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
[19/5754ae] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_REP1)
[e0/671aa3] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP2)
[85/999614] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP2)
[15/2abc3e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP1)
[22/250d41] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_IAA_30M_REP1)
[5f/91c2f5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP1)
[65/b6a935] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_UNINDUCED_REP2)
[c0/5c2f63] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (WT_REP2)
[5e/f80074] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_UNINDUCED_REP1)
[6b/ae7c31] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_IAA_30M_REP1)
[13/72af69] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (RAP1_UNINDUCED_REP2)
[b9/1463b1] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[dc/6a1d34] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (WT_REP2)
[16/9a179a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP2)
[89/4f4059] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (RAP1_UNINDUCED_REP1)
[7a/f7e82c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[77/c9e728] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (RAP1_IAA_30M_REP1)
[8a/8b7b06] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_IAA_30M_REP1)
[c6/4abfd6] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (WT_REP1)
[01/9019e1] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP2)
[2b/6e0891] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP1)
[2a/fcccb0] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP2)
[5d/7e6c50] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_REP1)
[4a/d19c6f] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[f9/2b64b7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP2)
[a8/6b120c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[31/3269fd] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1)
[91/d125c6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP2)
[19/babde9] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP2)
[25/4718b0] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_REP1)
[df/1a280f] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_IAA_30M_REP1)
[c4/02cb09] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[5d/8b76ca] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP1)
[05/14d461] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP1)
[f6/7feebb] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP1)
[bc/e0a130] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP1)
[a5/043791] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP1)
[cb/c38238] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP1)
[f4/acb95d] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP2)
[26/4de19f] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP2)
[35/58bd65] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP2)
[60/9c3fe7] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP2)
[f2/f31412] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[5b/dbd9fa] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP2)
[2f/9954ea] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP2)
[e0/816074] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (WT_REP1)
[c5/189ccf] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP1)
[c6/9aac66] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[b5/c0648a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_IAA_30M_REP1)
[02/fff059] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP1)
[ef/625a0f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP1)
[0e/45e2ad] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP1)
[1f/ea8969] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP1)
[d9/0a918c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP1)
[c6/f6e1ce] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP1)
[7c/d771a7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP1)
[a3/d6dc83] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP2)
[bd/807fa2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP2)
[3d/bf9080] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP2)
[f4/ebd77c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP2)
[7b/0f71ba] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP2)
[49/6151cb] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP2)
[69/5adfd7] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP2)
[c4/ff7dac] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[09/b99721] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP1)
[6e/a1d53f] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[5e/1b1026] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP2)
[3b/a70bfe] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[f0/6bf7a9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP2)
[fd/10c334] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP2)
[ec/0a967c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP2)
[f0/807817] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP2)
[f1/9e36b4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP2)
[b8/39c009] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP2)
[65/514c89] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP2)
[fa/061647] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[ce/8acf20] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE (null)
[5b/bc26c8] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[09/f19088] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_IAA_30M_REP1)
[66/884e6c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_IAA_30M_REP1)
[a7/f944bc] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_IAA_30M_REP1)
[47/f3db7d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_IAA_30M_REP1)
[f3/f25e92] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_IAA_30M_REP1)
[7b/9bfad5] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_IAA_30M_REP1)
[5a/1e772d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP2)
[bb/a57592] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP2)
[32/3b9753] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP2)
[3e/4cffd9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP2)
[7d/4c4837] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP2)
[32/9f8de8] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP2)
[b6/5547be] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP2)
[07/0c8a71] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP2)
[e1/d1ad34] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP2)
[da/ec38ba] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP2)
[7a/a90f31] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[c8/316314] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[8a/9b34ba] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[ad/e63db4] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[f6/ebf416] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT
[0d/5c54e1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_IAA_30M_REP1)
[c7/4ad4b6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_IAA_30M_REP1)
[69/370014] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_IAA_30M_REP1)
[b6/4ea295] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_IAA_30M_REP1)
[bf/41f0e8] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_IAA_30M_REP1)
[64/b9c22f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_IAA_30M_REP1)
[ee/ffa94b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_IAA_30M_REP1)
[4b/fcdfed] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP1)
[a8/902b04] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_MERGE_COUNTS
[23/4cd97e] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_IAA_30M_REP1)
[b8/2e728c] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[b8/0f6083] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[9b/16cdfe] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[7e/001f38] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[89/d5b753] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP1)
[93/ed9ce1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP1)
[fa/a17627] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_RSEM
[bc/acb949] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[ec/2a7c55] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[75/a23df8] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[08/c5a40e] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[00/25833f] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[e0/396bd2] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[46/1d8958] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[45/66baf6] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[97/69ce90] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[91/92f484] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[f3/1bdeb3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[3e/625d1d] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[93/bbe3ab] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[f1/163bc5] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[18/ac85a0] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[93/32949f] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[92/a29816] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[3e/eec570] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP1)
[ea/87cf64] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP1)
[d7/08d41d] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP1)
[b4/28a23a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP1)
[25/7f2779] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP1)
[aa/72f61f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP1)
[e5/979f68] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP1)
[b4/ca246d] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO
[c5/d3944a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED (all_samples)
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_RSEM'
Caused by:
Process `NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_RSEM` terminated with an error exit status (1)
Command executed:
deseq2_qc.r \
--count_file rsem.merged.gene_counts.tsv \
--outdir ./ \
--cores 2 \
--outprefix deseq2 \
--id_col 1 --sample_suffix '' --count_col 3 --vst TRUE
if [ -f "R_sessionInfo.log" ]; then
sed "s/deseq2_pca/star_rsem_deseq2_pca/g" <deseq2_pca_header.txt >tmp.txt
sed -i -e "s/DESeq2 PCA/STAR_RSEM DESeq2 PCA/g" tmp.txt
cat tmp.txt *.pca.vals.txt > star_rsem.pca.vals_mqc.tsv
sed "s/deseq2_clustering/star_rsem_deseq2_clustering/g" <deseq2_clustering_header.txt >tmp.txt
sed -i -e "s/DESeq2 sample/STAR_RSEM DESeq2 sample/g" tmp.txt
cat tmp.txt *.sample.dists.txt > star_rsem.sample.dists_mqc.tsv
fi
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_RSEM":
r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
bioconductor-deseq2: $(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))")
END_VERSIONS
Command exit status:
1
Command output:
null device
1
Command error:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
converting counts to integer mode
null device
1
.command.sh: line 14: tmp.txt: cannot overwrite existing file
Work dir:
/home/runner/work/rnaseq/rnaseq/~/tests/e9ed2c3496454a69937adc9eb340c688/work/fa/a17627fb802fc510f99450821bc193
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
-- Check '/home/runner/work/rnaseq/rnaseq/~/tests/e9ed2c3496454a69937adc9eb340c688/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/runner/work/rnaseq/rnaseq/~/tests/e9ed2c3496454a69937adc9eb340c688/meta/nextflow.log' file for details
-[0;35m[nf-core/rnaseq][0;31m Pipeline completed with errors[0m-
Nextflow stderr:
Nextflow 24.10.4 is available - Please consider updating your version to it
Loading