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GitHub Actions / JUnit Test Report failed Dec 10, 2024 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 controlfreec | somatic 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.11.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [silly_brenner] 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/d46f6304d77366be7c2f91242287e32/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
  wes                       : true
  tools                     : controlfreec

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
  chr_dir                   : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz
  dbsnp                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz
  dbsnp_tbi                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.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                   : silly_brenner
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32
  workDir                   : /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/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/d46f6304d77366be7c2f91242287e32/work/conda/env-b45f4430b1ab9d6e-f9b4f646bf1b67e52890543d27cb2f27]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/untar/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-e454bec5a9fe6279-cac18ad63488da9f5109ab1f794a29f6]
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/d46f6304d77366be7c2f91242287e32/work/conda/env-5a9ba0ebb7bcf86c-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/d46f6304d77366be7c2f91242287e32/work/conda/env-1abf3db016bf3fb9-873a3583ebab040412cb72c07ed757ab]
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/d46f6304d77366be7c2f91242287e32/work/conda/env-c5b497d07713b814-57cd7e91fe23a8ceb488416c37dae89b]
[f7/fd428e] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_mpileup/../../../modules/nf-core/samtools/mpileup/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-298b77ab5b2fec3c-873a3583ebab040412cb72c07ed757ab]
[b0/e0457a] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[2a/63bf43] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[28/5d053f] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[eb/7ffef9] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[1e/c0143c] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_2-23354000)
[b2/f440fe] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)
[01/11c21b] Submitted process > NFCORE_SAREK:PREPARE_GENOME:UNTAR_CHR_DIR (chromosomes.tar.gz)
[e5/5a8166] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_TUMOR:SAMTOOLS_MPILEUP (sample4_vs_sample3)
[e1/783f3d] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:SAMTOOLS_MPILEUP (sample4_vs_sample3)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_controlfreec/../../../modules/nf-core/controlfreec/freec/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-538bcdb3bc8da9e4-b045b606f9dcfe6897fe2c50e0f58bc7]
[c0/a20d2c] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:FREEC_SOMATIC (sample4_vs_sample3)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_controlfreec/../../../modules/nf-core/controlfreec/freec2bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-00cc74a07c8305aa-b045b606f9dcfe6897fe2c50e0f58bc7]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_controlfreec/../../../modules/nf-core/controlfreec/makegraph2/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-5c584a792008796d-b045b606f9dcfe6897fe2c50e0f58bc7]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_controlfreec/../../../modules/nf-core/controlfreec/freec2circos/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-4e8926983677b285-b045b606f9dcfe6897fe2c50e0f58bc7]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_controlfreec/../../../modules/nf-core/controlfreec/assesssignificance/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-ab3c40235a741d77-5b84389ee299f53755a38d176aa5b217]
[b6/79b751] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:FREEC2BED (sample4_vs_sample3)
[5a/df2fc5] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:ASSESS_SIGNIFICANCE (sample4_vs_sample3)
[b1/f8de4c] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:FREEC2CIRCOS (sample4_vs_sample3)
[89/76c738] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:MAKEGRAPH2 (sample4_vs_sample3)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/multiqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-7da4088df3b01749-eec4e05336245ea50db6412788f8c4da]
[e6/bc025b] Submitted process > NFCORE_SAREK:SAREK:MULTIQC
-[nf-core/sarek] Pipeline completed successfully-
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 manta,strelka --no_intervals | somatic 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.11.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [happy_brahmagupta] 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/d83ad9e6ce5149f25ccf62ff7c16f9a9/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
  no_intervals              : true
  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                   : happy_brahmagupta
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9
  workDir                   : /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/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/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-5a9ba0ebb7bcf86c-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/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-1abf3db016bf3fb9-873a3583ebab040412cb72c07ed757ab]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_manta/../../../modules/nf-core/manta/somatic/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f]
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/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-c5b497d07713b814-57cd7e91fe23a8ceb488416c37dae89b]
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/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-90ad7ffecab6b5bf-438a505d7b44a08705c858f9ad6e02ce]
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/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f]
[c7/bda83e] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (no_intervals)
[00/00c43e] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
[45/5e151f] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (sample3)
[00/00c43e] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)` terminated with an error exit status (1) -- Execution is retried (1)
[5e/734ebd] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
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/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-ac437bb99679f3c6-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/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-d14f40c429aefa2b-dc6f2c13cbbb0f956fd0966de87d7df8]
[83/674cdb] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[41/965748] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
[41/965748] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1) -- Execution is retried (1)
[05/0064f5] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[63/c01ace] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[0c/2a43b9] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample3)
[db/581927] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample3)
[bd/48e5df] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample3)
[38/d60c81] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample3)
[1f/db8868] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
[1f/db8868] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)` terminated with an error exit status (1) -- Execution is retried (2)
[92/528626] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
[92/528626] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1) -- Execution is retried (2)
[95/e4d206] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
[a8/d15cd6] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)` terminated with an error exit status (1)


Command executed:

  configManta.py \
      --bam test.paired_end.recalibrated.sorted.cram \
       \
      --reference genome.fasta \
      --runDir manta \
       \
  
  
  python manta/runWorkflow.py -m local -j 4
  
  mv manta/results/variants/candidateSmallIndels.vcf.gz \
      sample3.manta.candidate_small_indels.vcf.gz
  mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \
      sample3.manta.candidate_small_indels.vcf.gz.tbi
  mv manta/results/variants/candidateSV.vcf.gz \
      sample3.manta.candidate_sv.vcf.gz
  mv manta/results/variants/candidateSV.vcf.gz.tbi \
      sample3.manta.candidate_sv.vcf.gz.tbi
  mv manta/results/variants/diploidSV.vcf.gz \
      sample3.manta.diploid_sv.vcf.gz
  mv manta/results/variants/diploidSV.vcf.gz.tbi \
      sample3.manta.diploid_sv.vcf.gz.tbi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE":
      manta: $( configManta.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:
  
  manta/runWorkflow.py

Command error:
  [2024-12-10T18:06:23.574437Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] Adding command task 'sort_sortCandidateSV' to master workflow
  [2024-12-10T18:06:23.574669Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] Adding command task 'tabix_sortCandidateSV' to master workflow
  [2024-12-10T18:06:23.574879Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortDiploidSV' to master workflow
  [2024-12-10T18:06:23.575576Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] Adding sub-workflow task 'sortDiploidSVInputList' to master workflow
  [2024-12-10T18:06:23.576257Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] Adding command task 'sort_sortDiploidSV' to master workflow
  [2024-12-10T18:06:23.576466Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] Adding command task 'tabix_sortDiploidSV' to master workflow
  [2024-12-10T18:06:23.576721Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] Adding command task 'extractSmallIndels' to master workflow
  [2024-12-10T18:06:23.576940Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] Adding command task 'extractSmallIndels_tabix' to master workflow
  [2024-12-10T18:06:23.577428Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] Adding sub-workflow task 'sortEdgeRuntimeLogsInputList' to master workflow
  [2024-12-10T18:06:23.578296Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] Adding command task 'sortEdgeRuntimeLogs' to master workflow
  [2024-12-10T18:06:23.578439Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
  [2024-12-10T18:06:23.611292Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] Completed command task: 'getAlignmentStats_makeTmpDir' launched from master workflow
  [2024-12-10T18:06:23.611362Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] Completed command task: 'getChromDepth_makeTmpDir' launched from master workflow
  [2024-12-10T18:06:23.611923Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] Launching command task: 'getChromDepth_sample000_makeTmpDir' from master workflow
  [2024-12-10T18:06:23.612157Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_000' from master workflow
  [2024-12-10T18:06:23.614968Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getChromDepth_sample000_makeTmpDir] Task initiated on local node
  [2024-12-10T18:06:23.615794Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
  [2024-12-10T18:06:23.646423Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getAlignmentStats_generateStats_000] [WARNING] Task: 'getAlignmentStats_generateStats_000' failed but qualifies for retry. Total task failures (including this one): 1. Task command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
  [2024-12-10T18:06:23.676305Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] Completed command task: 'getChromDepth_sample000_makeTmpDir' launched from master workflow
  [2024-12-10T18:06:23.677035Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] Launching command task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' from master workflow
  [2024-12-10T18:06:23.679323Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
  [2024-12-10T18:06:23.705489Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] [WARNING] Task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' failed but qualifies for retry. Total task failures (including this one): 1. Task command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth --ref genome.fasta --align-file test.paired_end.recalibrated.sorted.cram --output manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chr21 --chrom chr21'
  [2024-12-10T18:07:53.651273Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getAlignmentStats_generateStats_000] Retrying task: 'getAlignmentStats_generateStats_000'. Total prior task failures: 1
  [2024-12-10T18:07:53.653841Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
  [2024-12-10T18:07:53.680964Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getAlignmentStats_generateStats_000] [WARNING] Task: 'getAlignmentStats_generateStats_000' failed but qualifies for retry. Total task failures (including this one): 2. Task command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
  [2024-12-10T18:07:53.795636Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Retrying task: 'getChromDepth_sample000_estimateChromDepth_000_chr21'. Total prior task failures: 1
  [2024-12-10T18:07:53.797965Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
  [2024-12-10T18:07:53.824022Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] [WARNING] Task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' failed but qualifies for retry. Total task failures (including this one): 2. Task command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth --ref genome.fasta --align-file test.paired_end.recalibrated.sorted.cram --output manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chr21 --chrom chr21'
  [2024-12-10T18:09:23.765317Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getAlignmentStats_generateStats_000] Retrying task: 'getAlignmentStats_generateStats_000'. Total prior task failures: 2
  [2024-12-10T18:09:23.767759Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
  [2024-12-10T18:09:23.815565Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
  [2024-12-10T18:09:23.815853Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
  [2024-12-10T18:09:23.815903Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-10T18:09:23.815903Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] [ERROR] [2024-12-10T18:09:23.789971Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [getAlignmentStats_generateStats_000] /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
  [2024-12-10T18:09:23.815951Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
  [2024-12-10T18:09:23.914596Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Retrying task: 'getChromDepth_sample000_estimateChromDepth_000_chr21'. Total prior task failures: 2
  [2024-12-10T18:09:23.916755Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
  [2024-12-10T18:09:23.980178Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth --ref genome.fasta --align-file test.paired_end.recalibrated.sorted.cram --output manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chr21 --chrom chr21'
  [2024-12-10T18:09:23.980248Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Error Message:
  [2024-12-10T18:09:23.980271Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-10T18:09:23.980271Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [TaskManager] [ERROR] [2024-12-10T18:09:23.939770Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [getChromDepth_sample000_estimateChromDepth_000_chr21] /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
  [2024-12-10T18:09:26.829307Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
  [2024-12-10T18:09:26.829389Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
  [2024-12-10T18:09:26.829428Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
  [2024-12-10T18:09:26.829469Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-10T18:09:26.829469Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] [ERROR] [2024-12-10T18:09:23.789971Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [getAlignmentStats_generateStats_000] /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
  [2024-12-10T18:09:26.829526Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth --ref genome.fasta --align-file test.paired_end.recalibrated.sorted.cram --output manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chr21 --chrom chr21'
  [2024-12-10T18:09:26.829576Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Error Message:
  [2024-12-10T18:09:26.829608Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-10T18:09:26.829608Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [WorkflowRunner] [ERROR] [2024-12-10T18:09:23.939770Z] [fv-az1020-352.iv4l2o2nioduhiqnghm4updqgd.ex.internal.cloudapp.net] [131874_1] [getChromDepth_sample000_estimateChromDepth_000_chr21] /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory

Work dir:
  /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/95/e4d206292b3ee6c7956ceae91efe63

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/d83ad9e6ce5149f25ccf62ff7c16f9a9/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/d83ad9e6ce5149f25ccf62ff7c16f9a9/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/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-7da4088df3b01749-eec4e05336245ea50db6412788f8c4da]
Nextflow stderr:
View more details on GitHub Actions