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Release 3.5.1 #1799

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merged 13 commits into from
Feb 18, 2025

Update .github/workflows/cloudtest.yml

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Merged

Release 3.5.1 #1799

Update .github/workflows/cloudtest.yml
04cbd12
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GitHub Actions / JUnit Test Report failed Feb 17, 2025 in 0s

9 tests run, 7 passed, 0 skipped, 2 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 | --tools merge,snpeff,vep 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 25.01.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [stupefied_cray] DSL2 - revision: 3954909713

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

  nf-core/sarek 3.5.1
------------------------------------------------------
Input/output options
  input                     : /home/runner/work/sarek/sarek/tests/csv/3.0/vcf_single.csv
  step                      : annotate
  outdir                    : /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/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                     : merge,snpeff,vep

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_db                 : WBcel235.105
  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                   : stupefied_cray
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87
  workDir                   : /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,conda
  configFiles               : /home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/conf/test.config

!! 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

Staging foreign file: s3://annotation-cache/snpeff_cache/WBcel235.105
Staging foreign file: s3://annotation-cache/vep_cache/113_WBcel235
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_annotate_all/../../nf-core/vcf_annotate_snpeff/../../../modules/nf-core/snpeff/snpeff/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-f166f6710d1284fe-45d87f58d9b67245610a395695fff284]
[7b/5dbba7] Submitted process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_annotate_all/../../nf-core/vcf_annotate_ensemblvep/../../../modules/nf-core/ensemblvep/vep/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_annotate_all/../../nf-core/vcf_annotate_snpeff/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-5a9ba0ebb7bcf86c-497b0f18c811c5671b5e17e0034188ed]
[cb/93c404] Submitted process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP (test)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP (test)'

Caused by:
  Process `NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP (test)` terminated with an error exit status (2)


Command executed:

  vep \
      -i test.vcf.gz \
      -o test_VEP.ann.vcf.gz \
      --stats_file test_VEP.ann.summary.html      --vcf --everything --filter_common --per_gene --total_length --offline --format vcf \
      --compress_output bgzip \
       \
      --assembly WBcel235 \
      --species caenorhabditis_elegans \
      --cache \
      --cache_version 113 \
      --dir_cache ${PWD}/113_WBcel235 \
      --fork 4
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP":
      ensemblvep: $( echo $(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*$//')
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  Can't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/modules /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0 /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/5.32/site_perl /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/site_perl /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/5.32/vendor_perl /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/vendor_perl /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/5.32/core_perl /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/core_perl .) at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 102.
  BEGIN failed--compilation aborted at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 102.
  Compilation failed in require at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
  BEGIN failed--compilation aborted at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
  Compilation failed in require at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/vendor_perl/base.pm line 100.
  	...propagated at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/vendor_perl/base.pm line 109.
  BEGIN failed--compilation aborted at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm line 56.
  Compilation failed in require at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/vendor_perl/base.pm line 100.
  	...propagated at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/vendor_perl/base.pm line 109.
  BEGIN failed--compilation aborted at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/modules/Bio/EnsEMBL/VEP/Runner.pm line 71.
  Compilation failed in require at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/bin/vep line 20.
  BEGIN failed--compilation aborted at /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/bin/vep line 20.

Work dir:
  /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/cb/93c404bae87b20de41b9756e345f88

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/a6eae50a4c682d0c3809489d21e5ad87/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/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/meta/nextflow.log' file for details
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/multiqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/a6eae50a4c682d0c3809489d21e5ad87/work/conda/env-7da4088df3b01749-eec4e05336245ea50db6412788f8c4da]
-[nf-core/sarek] Pipeline completed with errors-
Nextflow stderr:

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 | somatic 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 25.01.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [mighty_descartes] DSL2 - revision: 3954909713

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

  nf-core/sarek 3.5.1
------------------------------------------------------
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/905ea0e770881b92655672a0f2677138/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

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_descartes
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138
  workDir                   : /home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,conda
  configFiles               : /home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/conf/test.config

!! 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/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/conda/env-5a9ba0ebb7bcf86c-497b0f18c811c5671b5e17e0034188ed]
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/905ea0e770881b92655672a0f2677138/work/conda/env-b45f4430b1ab9d6e-47b5d3c40746bfdb673888286797637b]
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta
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/905ea0e770881b92655672a0f2677138/work/conda/env-c5b497d07713b814-57cd7e91fe23a8ceb488416c37dae89b]
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/905ea0e770881b92655672a0f2677138/work/conda/env-1abf3db016bf3fb9-873a3583ebab040412cb72c07ed757ab]
[30/6633b3] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)
[b6/cba4a9] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[72/53a2f6] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[87/2ae42a] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[51/2128a4] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[7e/b23376] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[2d/cc31fa] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_2-23354000)
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/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce]
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/905ea0e770881b92655672a0f2677138/work/conda/env-90ad7ffecab6b5bf-438a505d7b44a08705c858f9ad6e02ce]
[c1/788adf] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)
[ce/28e636] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (sample3)
[c1/788adf] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1) -- Execution is retried (1)
[c1/a14c73] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)
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/905ea0e770881b92655672a0f2677138/work/conda/env-d14f40c429aefa2b-dc6f2c13cbbb0f956fd0966de87d7df8]
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/905ea0e770881b92655672a0f2677138/work/conda/env-ac437bb99679f3c6-ede778c78582be405557f3c8ca0e9927]
[c1/a14c73] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1) -- Execution is retried (2)
[18/f76cf0] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample3)
[88/c02214] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)
[c9/b5ffee] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample3)
[ea/e7f104] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample3)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1)


Command executed:

  configureStrelkaSomaticWorkflow.py \
      --tumor test2.paired_end.recalibrated.sorted.cram \
      --normal test.paired_end.recalibrated.sorted.cram \
      --referenceFasta genome.fasta \
      --callRegions chr21_2-23354000.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     sample4_vs_sample3.strelka.somatic_indels.vcf.gz
  mv strelka/results/variants/somatic.indels.vcf.gz.tbi sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
  mv strelka/results/variants/somatic.snvs.vcf.gz       sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
  mv strelka/results/variants/somatic.snvs.vcf.gz.tbi   sample4_vs_sample3.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:
  [2025-02-17T18:21:17.790507Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:21:17.765852Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStderrTail 1
  [2025-02-17T18:21:17.790524Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
  [2025-02-17T18:21:17.790631Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:1-11677496 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.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/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
  [2025-02-17T18:21:17.790675Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Error Message:
  [2025-02-17T18:21:17.790696Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
  [2025-02-17T18:21:17.790714Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Logging 5 line(s) of task wrapper log output below:
  [2025-02-17T18:21:17.790747Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:21:17.512239Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] wrapperStart
  [2025-02-17T18:21:17.790774Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:21:17.523407Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStart
  [2025-02-17T18:21:17.790791Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:21:17.773574Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskExitCode -11
  [2025-02-17T18:21:17.790813Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:21:17.775273Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStderrTail 1
  [2025-02-17T18:21:17.790830Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
  [2025-02-17T18:21:18.458152Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
  [2025-02-17T18:21:21.079090Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
  [2025-02-17T18:21:21.079156Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0003' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:35032489-46709983 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.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/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0003.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0003.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0003.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
  [2025-02-17T18:21:21.079210Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Error Message:
  [2025-02-17T18:21:21.079229Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/015/pyflowTaskWrapper.signal.txt'
  [2025-02-17T18:21:21.079253Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Logging 5 line(s) of task wrapper log output below:
  [2025-02-17T18:21:21.079277Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:21:17.514962Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] wrapperStart
  [2025-02-17T18:21:21.079298Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:21:17.530453Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStart
  [2025-02-17T18:21:21.079322Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:21:17.762489Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskExitCode -11
  [2025-02-17T18:21:21.079349Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:21:17.765852Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStderrTail 1
  [2025-02-17T18:21:21.079373Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
  [2025-02-17T18:21:21.079396Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:1-11677496 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.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/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
  [2025-02-17T18:21:21.079429Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Error Message:
  [2025-02-17T18:21:21.079445Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
  [2025-02-17T18:21:21.079469Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Logging 5 line(s) of task wrapper log output below:
  [2025-02-17T18:21:21.079490Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:21:17.512239Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] wrapperStart
  [2025-02-17T18:21:21.079512Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:21:17.523407Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStart
  [2025-02-17T18:21:21.079533Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:21:17.773574Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskExitCode -11
  [2025-02-17T18:21:21.079558Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:21:17.775273Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStderrTail 1
  [2025-02-17T18:21:21.079581Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
  [2025-02-17T18:21:21.079602Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
  [2025-02-17T18:21:21.079622Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0001' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:11677497-23354992 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.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/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0001.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0001.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0001.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
  [2025-02-17T18:21:21.079654Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Error Message:
  [2025-02-17T18:21:21.079679Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/011/pyflowTaskWrapper.signal.txt'
  [2025-02-17T18:21:21.079702Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Logging 5 line(s) of task wrapper log output below:
  [2025-02-17T18:21:21.079723Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:21:17.514278Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] wrapperStart
  [2025-02-17T18:21:21.079768Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:21:17.524105Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStart
  [2025-02-17T18:21:21.079791Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:21:17.717915Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskExitCode -11
  [2025-02-17T18:21:21.079813Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:21:17.722795Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStderrTail 1
  [2025-02-17T18:21:21.079842Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
  [2025-02-17T18:21:21.079867Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0002' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:23354993-35032488 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.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/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0002.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0002.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0002.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
  [2025-02-17T18:21:21.079898Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Error Message:
  [2025-02-17T18:21:21.079914Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/013/pyflowTaskWrapper.signal.txt'
  [2025-02-17T18:21:21.079934Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Logging 5 line(s) of task wrapper log output below:
  [2025-02-17T18:21:21.079958Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:21:17.511884Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] wrapperStart
  [2025-02-17T18:21:21.079980Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:21:17.521315Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskStart
  [2025-02-17T18:21:21.080001Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:21:17.725106Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskExitCode -11
  [2025-02-17T18:21:21.080022Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:21:17.731470Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskStderrTail 1
  [2025-02-17T18:21:21.080047Z] [fv-az1371-407.usr2iisjv3qe3alikr1tape2yd.ex.internal.cloudapp.net] [133149_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):

Work dir:
  /home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/work/88/c02214729305020b3128b04e28f30d

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '/home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/meta/nextflow.log' file for details
[e8/c509dd] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample3)
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/sarek/sarek/~/tests/905ea0e770881b92655672a0f2677138/meta/nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-
WARN: Killing running tasks (3)
Nextflow stderr:
View more details on GitHub Actions