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Merge pull request #1755 from FriederikeHanssen/localmod #6952

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Merge pull request #1755 from FriederikeHanssen/localmod

Merge pull request #1755 from FriederikeHanssen/localmod #6952

GitHub Actions / JUnit Test Report failed Dec 11, 2024 in 0s

9 tests run, 6 passed, 0 skipped, 3 failed.

Annotations

Check failure on line 1 in Test pipeline

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline.Run with profile test | --input tests/csv/3.0/fastq_pair.csv 

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/sarek/sarek/tests/../main.nf` [distraught_swirles] DSL2 - revision: 3954909713

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek 3.5.0
------------------------------------------------------
Input/output options
  input                     : /home/runner/work/sarek/sarek/tests/csv/3.0/fastq_pair.csv
  outdir                    : /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/output

Main options
  split_fastq               : 0
  intervals                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.interval_list
  tools                     : strelka

Annotation
  bcftools_annotations      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz
  bcftools_annotations_tbi  : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi
  bcftools_header_lines     : /home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt

General reference genome options
  igenomes_base             : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Reference genome options
  genome                    : testdata.nf-core.sarek
  dbsnp                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi
  dbsnp_vqsr                : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
  dict                      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.fasta
  fasta_fai                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.fasta.fai
  germline_resource         : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz
  germline_resource_tbi     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi
  known_indels              : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
  known_indels_tbi          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi
  known_indels_vqsr         : --resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz
  ngscheckmate_bed          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed
  sentieon_dnascope_model   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
  snpeff_cache              : null
  snpeff_db                 : WBcel235.105
  vep_cache                 : null
  vep_cache_version         : 113
  vep_genome                : WBcel235
  vep_species               : caenorhabditis_elegans

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
  modules_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Core Nextflow options
  runName                   : distraught_swirles
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0
  workDir                   : /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,conda
  configFiles               : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.12688/f1000research.16665.2
    https://doi.org/10.1093/nargab/lqae031
    https://doi.org/10.5281/zenodo.3476425

* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/sarek/blob/master/CITATIONS.md

WARN: FASTQ file(/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz): Cannot extract flowcell ID from @normal#21#998579#1/1
WARN: FASTQ file(/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz): Cannot extract flowcell ID from @normal#21#998513#1/1
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/bwa/index/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-b7d45abbc59134ec734c2810969e7f00]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-47b5d3c40746bfdb673888286797637b]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/gatk4/intervallisttobed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-d2d82a1cc7858810940ff84273e57b63]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/fastqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-3ea42529974ca5a54ae5623eacfbc76a]
[4a/a42993] Submitted process > NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX (genome.fasta)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/../../../modules/nf-core/bwa/mem/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-302c740918ed3eabd6af342133129057]
[50/ac65d9] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test-test_L1)
[5f/fab21a] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test2-test_L1)
[38/fab72c] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED (genome)
[22/b562f2] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (genome.interval_list)
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-497b0f18c811c5671b5e17e0034188ed]
[50/8e524b] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test2)
[ec/3ef542] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../../../modules/nf-core/gatk4/markduplicates/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-7753f12b1b6af37c6e7eb5fd03e42240]
[e7/e55ca5] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr22_1-40001)
[67/a10b57] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (genome)
[f6/d8e497] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (test)
[c3/5a5f42] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (test2)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-873a3583ebab040412cb72c07ed757ab]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-57cd7e91fe23a8ceb488416c37dae89b]
[e5/025958] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test)
[5a/b68687] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test)
[78/5a8fa0] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test2)
[68/f447b6] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test2)
[ff/8b9815] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test)
[35/7422ba] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test2)
[98/5f27e0] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_single_strelka/../../../modules/nf-core/strelka/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce]
[35/aa9b83] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (test)
[18/4c6b22] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (test)
[07/fb8688] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (test2)
[84/ec2ece] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (test)
[af/403997] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test2)
[78/400b78] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (test2)
[d8/a9103b] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (test2)
[6b/60786a] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)
[00/05c3b3] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (test)
[6b/60786a] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)` terminated with an error exit status (1) -- Execution is retried (1)
[82/6d3a5f] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_qc_bcftools_vcftools/../../../modules/nf-core/vcftools/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-ede778c78582be405557f3c8ca0e9927]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_qc_bcftools_vcftools/../../../modules/nf-core/bcftools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-dc6f2c13cbbb0f956fd0966de87d7df8]
[82/6d3a5f] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)` terminated with an error exit status (1) -- Execution is retried (2)
[09/e93f9b] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (test)
[5d/686530] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (test)
[a6/a454f4] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (test)
[74/a4f8b1] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)
[33/e37c61] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (test)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)` terminated with an error exit status (1)


Command executed:

  configureStrelkaSomaticWorkflow.py \
      --tumor test2.recal.cram \
      --normal test.recal.cram \
      --referenceFasta genome.fasta \
      --callRegions chr22_1-40001.bed.gz \
       \
       \
      --runDir strelka
  
  sed -i s/"isEmail = isLocalSmtp()"/"isEmail = False"/g strelka/runWorkflow.py
  
  python strelka/runWorkflow.py -m local -j 4
  mv strelka/results/variants/somatic.indels.vcf.gz     test2_vs_test.strelka.somatic_indels.vcf.gz
  mv strelka/results/variants/somatic.indels.vcf.gz.tbi test2_vs_test.strelka.somatic_indels.vcf.gz.tbi
  mv strelka/results/variants/somatic.snvs.vcf.gz       test2_vs_test.strelka.somatic_snvs.vcf.gz
  mv strelka/results/variants/somatic.snvs.vcf.gz.tbi   test2_vs_test.strelka.somatic_snvs.vcf.gz.tbi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC":
      strelka: $( configureStrelkaSomaticWorkflow.py --version )
  END_VERSIONS

Command exit status:
  1

Command output:
  
  Successfully created workflow run script.
  To execute the workflow, run the following script and set appropriate options:
  
  strelka/runWorkflow.py

Command error:
  [2024-12-11T18:02:50.914183Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] Launching command task: 'getChromDepth_sample000_catChromDepth' from master workflow
  [2024-12-11T18:02:50.916438Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskRunner:getChromDepth_sample000_catChromDepth] Task initiated on local node
  [2024-12-11T18:02:50.977931Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] Completed command task: 'getChromDepth_sample000_catChromDepth' launched from master workflow
  [2024-12-11T18:02:50.978201Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] Launching command task: 'getChromDepth_mergeChromDepth' from master workflow
  [2024-12-11T18:02:50.980314Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskRunner:getChromDepth_mergeChromDepth] Task initiated on local node
  [2024-12-11T18:02:51.041952Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] Completed command task: 'getChromDepth_mergeChromDepth' launched from master workflow
  [2024-12-11T18:02:51.042182Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
  [2024-12-11T18:02:51.042336Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
  [2024-12-11T18:02:51.042747Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.043104Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] Launching command task: 'getChromDepth_removeTmpDir' from master workflow
  [2024-12-11T18:02:51.043385Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.044201Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.046436Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.046955Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.047067Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskRunner:getChromDepth_removeTmpDir] Task initiated on local node
  [2024-12-11T18:02:51.047273Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.047787Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.048154Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.048918Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.049374Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.051685Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.051914Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.052175Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
  [2024-12-11T18:02:51.053112Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
  [2024-12-11T18:02:51.084559Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] Completed command task: 'getChromDepth_removeTmpDir' launched from master workflow
  [2024-12-11T18:02:51.092157Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.092464Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' from sub-workflow 'CallGenome'
  [2024-12-11T18:02:51.094757Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_000_chr22_0000] Task initiated on local node
  [2024-12-11T18:02:51.256541Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr22:1-40001 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr22_1-40001.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.recal.cram --tumor-align-file test2.recal.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr22_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr22_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr22_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
  [2024-12-11T18:02:51.256638Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Error Message:
  [2024-12-11T18:02:51.256659Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
  [2024-12-11T18:02:51.256676Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Logging 5 line(s) of task wrapper log output below:
  [2024-12-11T18:02:51.256695Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T18:02:51.109205Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] wrapperStart
  [2024-12-11T18:02:51.256725Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T18:02:51.118810Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStart
  [2024-12-11T18:02:51.256746Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T18:02:51.203452Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskExitCode -11
  [2024-12-11T18:02:51.256759Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T18:02:51.204939Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStderrTail 1
  [2024-12-11T18:02:51.256773Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
  [2024-12-11T18:02:51.256792Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
  [2024-12-11T18:02:52.071819Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
  [2024-12-11T18:02:53.488735Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
  [2024-12-11T18:02:53.488771Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr22:1-40001 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr22_1-40001.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.recal.cram --tumor-align-file test2.recal.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr22_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr22_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr22_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
  [2024-12-11T18:02:53.488803Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Error Message:
  [2024-12-11T18:02:53.488816Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
  [2024-12-11T18:02:53.488830Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Logging 5 line(s) of task wrapper log output below:
  [2024-12-11T18:02:53.488844Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T18:02:51.109205Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] wrapperStart
  [2024-12-11T18:02:53.488862Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T18:02:51.118810Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStart
  [2024-12-11T18:02:53.488877Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T18:02:51.203452Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskExitCode -11
  [2024-12-11T18:02:53.488894Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T18:02:51.204939Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStderrTail 1
  [2024-12-11T18:02:53.488907Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
  [2024-12-11T18:02:53.488925Z] [fv-az1771-164.2ylvbwgxy3nupokun4gfpak4pb.dx.internal.cloudapp.net] [124261_1] [WorkflowRunner] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'

Work dir:
  /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/74/a4f8b137b6566d7723e0aef90827cd

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/meta/nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-
WARN: Killing running tasks (1)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/multiqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-eec4e05336245ea50db6412788f8c4da]
Nextflow stderr:

Nextflow 24.10.2 is available - Please consider updating your version to it

Check failure on line 1 in Test pipeline

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline.Run with profile test | --tools strelka --only_paired_variant_calling 

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/sarek/sarek/tests/../main.nf` [elated_lamport] DSL2 - revision: 3954909713

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek 3.5.0
------------------------------------------------------
Input/output options
  input                      : /home/runner/work/sarek/sarek/tests/csv/3.0/recalibrated.csv
  step                       : variant_calling
  outdir                     : /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/output

Main options
  split_fastq                : 0
  intervals                  : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed
  tools                      : strelka

Variant Calling
  only_paired_variant_calling: true

Annotation
  bcftools_annotations       : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz
  bcftools_annotations_tbi   : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi
  bcftools_header_lines      : /home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt

General reference genome options
  igenomes_base              : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Reference genome options
  genome                     : testdata.nf-core.sarek
  dbsnp                      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi                  : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi
  dbsnp_vqsr                 : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
  dict                       : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict
  fasta                      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta
  fasta_fai                  : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai
  germline_resource          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz
  germline_resource_tbi      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi
  known_indels               : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
  known_indels_tbi           : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi
  known_indels_vqsr          : --resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz
  ngscheckmate_bed           : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed
  sentieon_dnascope_model    : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
  snpeff_cache               : null
  snpeff_db                  : WBcel235.105
  vep_cache                  : null
  vep_cache_version          : 113
  vep_genome                 : WBcel235
  vep_species                : caenorhabditis_elegans

Institutional config options
  config_profile_name        : Test profile
  config_profile_description : Minimal test dataset to check pipeline function
  modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Core Nextflow options
  runName                    : elated_lamport
  launchDir                  : /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132
  workDir                    : /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work
  projectDir                 : /home/runner/work/sarek/sarek
  userName                   : runner
  profile                    : test,conda
  configFiles                : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.12688/f1000research.16665.2
    https://doi.org/10.1093/nargab/lqae031
    https://doi.org/10.5281/zenodo.3476425

* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/sarek/blob/master/CITATIONS.md

Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/environment-47b5d3c40746bfdb673888286797637b]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/environment-497b0f18c811c5671b5e17e0034188ed]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/environment-873a3583ebab040412cb72c07ed757ab]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/environment-57cd7e91fe23a8ceb488416c37dae89b]
[ba/93c41e] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[9d/603484] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[f6/65a391] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[01/b8d820] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample1)
[3e/a59d0a] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample2)
[ad/f02d8f] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[54/b823d1] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample1)
[c0/ebe55a] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_2-23354000)
[f1/f3c485] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_strelka/../../../modules/nf-core/strelka/somatic/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce]
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (1)'

Caused by:
  java.nio.channels.OverlappingFileLockException



 -- Check '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/meta/nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-
WARN: Killing running tasks (2)
Nextflow stderr:

Nextflow 24.10.2 is available - Please consider updating your version to it

Check failure on line 1 in Test pipeline

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline.Run with profile test | --tools manta,strelka | somatic 

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/sarek/sarek/tests/../main.nf` [mighty_williams] DSL2 - revision: 3954909713

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek 3.5.0
------------------------------------------------------
Input/output options
  input                     : /home/runner/work/sarek/sarek/tests/csv/3.0/recalibrated_somatic.csv
  step                      : variant_calling
  outdir                    : /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/output

Main options
  split_fastq               : 0
  intervals                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed
  tools                     : manta,strelka

Annotation
  bcftools_annotations      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz
  bcftools_annotations_tbi  : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi
  bcftools_header_lines     : /home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt

General reference genome options
  igenomes_base             : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Reference genome options
  genome                    : testdata.nf-core.sarek
  dbsnp                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi
  dbsnp_vqsr                : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
  dict                      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta
  fasta_fai                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai
  germline_resource         : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz
  germline_resource_tbi     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi
  known_indels              : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
  known_indels_tbi          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi
  known_indels_vqsr         : --resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz
  ngscheckmate_bed          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed
  sentieon_dnascope_model   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
  snpeff_cache              : null
  snpeff_db                 : WBcel235.105
  vep_cache                 : null
  vep_cache_version         : 113
  vep_genome                : WBcel235
  vep_species               : caenorhabditis_elegans

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
  modules_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Core Nextflow options
  runName                   : mighty_williams
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60
  workDir                   : /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,conda
  configFiles               : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.12688/f1000research.16665.2
    https://doi.org/10.1093/nargab/lqae031
    https://doi.org/10.5281/zenodo.3476425

* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/sarek/blob/master/CITATIONS.md

Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-47b5d3c40746bfdb673888286797637b]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-497b0f18c811c5671b5e17e0034188ed]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-57cd7e91fe23a8ceb488416c37dae89b]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-873a3583ebab040412cb72c07ed757ab]
[ff/5b5a5c] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[fe/0cb945] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[31/8a240a] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[36/4301e2] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[41/c29b09] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[88/7f8dd1] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_2-23354000)
[09/4d322f] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_germline_manta/../../../modules/nf-core/manta/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-86f8fc4b934d0b08515f88ef4592bd1f]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_single_strelka/../../../modules/nf-core/strelka/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce]
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (1)'

Caused by:
  java.nio.channels.OverlappingFileLockException



 -- Check '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/meta/nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-
Join mismatch for the following entries: key=[id:sample4_vs_sample3, normal_id:sample3, patient:test3, sex:XX, tumor_id:sample4] values=


Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/multiqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-eec4e05336245ea50db6412788f8c4da]
Nextflow stderr:

Nextflow 24.10.2 is available - Please consider updating your version to it
View more details on GitHub Actions