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Merge pull request #1748 from FriederikeHanssen/release_350 #6936

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Merge pull request #1748 from FriederikeHanssen/release_350

Merge pull request #1748 from FriederikeHanssen/release_350 #6936

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` [peaceful_monod] 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                   : peaceful_monod
  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/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/./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/./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]
[bd/1359f7] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)
[67/22410c] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[08/6d19e2] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[be/f428a0] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[c3/4f6029] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[71/673986] Submitted process > NFCORE_SAREK:PREPARE_GENOME:UNTAR_CHR_DIR (chromosomes.tar.gz)
[c5/5c4d28] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[22/e01e0c] 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_mpileup/../../../modules/nf-core/samtools/mpileup/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-298b77ab5b2fec3c-873a3583ebab040412cb72c07ed757ab]
[e7/c86afc] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:SAMTOOLS_MPILEUP (sample4_vs_sample3)
[9c/902ac9] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_TUMOR: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]
[af/885b93] 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/assesssignificance/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-ab3c40235a741d77-5b84389ee299f53755a38d176aa5b217]
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/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/makegraph2/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-5c584a792008796d-b045b606f9dcfe6897fe2c50e0f58bc7]
[a6/dda820] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:ASSESS_SIGNIFICANCE (sample4_vs_sample3)
[34/d000b8] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:MAKEGRAPH2 (sample4_vs_sample3)
[40/e2b993] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:FREEC2CIRCOS (sample4_vs_sample3)
[64/07edcf] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:FREEC2BED (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]
[e2/f0025d] 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` [tender_shirley] 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                   : tender_shirley
  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_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]
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_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/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]
[0c/ce0f5a] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (no_intervals)
[62/3cb1d8] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (sample3)
[7b/85495c] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_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/d83ad9e6ce5149f25ccf62ff7c16f9a9/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/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-ac437bb99679f3c6-ede778c78582be405557f3c8ca0e9927]
[84/0e6533] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[7b/85495c] 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)
[e7/88c72a] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[c1/352c76] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
[c1/352c76] 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)
[18/7a1542] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[e5/515aa8] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[6f/304302] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample3)
[fa/890460] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample3)
[cb/6460d6] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample3)
[b7/7d6bfb] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample3)
[16/405dc3] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
[16/405dc3] 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)
[f0/bdac65] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
[f0/bdac65] 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)
[98/8dd4a2] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
[26/21c93b] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)'

Caused by:
  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)


Command executed:

  configManta.py \
      --tumorBam test2.paired_end.recalibrated.sorted.cram \
      --normalBam 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 \
      sample4_vs_sample3.manta.candidate_small_indels.vcf.gz
  mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \
      sample4_vs_sample3.manta.candidate_small_indels.vcf.gz.tbi
  mv manta/results/variants/candidateSV.vcf.gz \
      sample4_vs_sample3.manta.candidate_sv.vcf.gz
  mv manta/results/variants/candidateSV.vcf.gz.tbi \
      sample4_vs_sample3.manta.candidate_sv.vcf.gz.tbi
  mv manta/results/variants/diploidSV.vcf.gz \
      sample4_vs_sample3.manta.diploid_sv.vcf.gz
  mv manta/results/variants/diploidSV.vcf.gz.tbi \
      sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
  mv manta/results/variants/somaticSV.vcf.gz \
      sample4_vs_sample3.manta.somatic_sv.vcf.gz
  mv manta/results/variants/somaticSV.vcf.gz.tbi \
      sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC":
      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:
  [2024-12-10T13:20:01.536309Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getChromDepth_sample000_makeTmpDir] Task initiated on local node
  [2024-12-10T13:20:01.538242Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_001] Task initiated on local node
  [2024-12-10T13:20:01.539944Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
  [2024-12-10T13:20:01.572760Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_001] [WARNING] Task: 'getAlignmentStats_generateStats_001' failed but qualifies for retry. Total task failures (including this one): 1. Task command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.001.xml --align-file test2.paired_end.recalibrated.sorted.cram'
  [2024-12-10T13:20:01.575143Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_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-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
  [2024-12-10T13:20:01.597019Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] Completed command task: 'getChromDepth_sample000_makeTmpDir' launched from master workflow
  [2024-12-10T13:20:01.597702Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] Launching command task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' from master workflow
  [2024-12-10T13:20:01.600072Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
  [2024-12-10T13:20:01.627682Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_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-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/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'
  [2024-12-10T13:21:31.593634Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_001] Retrying task: 'getAlignmentStats_generateStats_001'. Total prior task failures: 1
  [2024-12-10T13:21:31.593806Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_000] Retrying task: 'getAlignmentStats_generateStats_000'. Total prior task failures: 1
  [2024-12-10T13:21:31.596268Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_001] Task initiated on local node
  [2024-12-10T13:21:31.597006Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
  [2024-12-10T13:21:31.625155Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_001] [WARNING] Task: 'getAlignmentStats_generateStats_001' failed but qualifies for retry. Total task failures (including this one): 2. Task command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.001.xml --align-file test2.paired_end.recalibrated.sorted.cram'
  [2024-12-10T13:21:31.625384Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_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-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
  [2024-12-10T13:21:31.693570Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Retrying task: 'getChromDepth_sample000_estimateChromDepth_000_chr21'. Total prior task failures: 1
  [2024-12-10T13:21:31.695720Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
  [2024-12-10T13:21:31.722167Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_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-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/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'
  [2024-12-10T13:23:01.689008Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_000] Retrying task: 'getAlignmentStats_generateStats_000'. Total prior task failures: 2
  [2024-12-10T13:23:01.691519Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
  [2024-12-10T13:23:01.715314Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_001] Retrying task: 'getAlignmentStats_generateStats_001'. Total prior task failures: 2
  [2024-12-10T13:23:01.717845Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getAlignmentStats_generateStats_001] Task initiated on local node
  [2024-12-10T13:23:01.739332Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_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-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
  [2024-12-10T13:23:01.739559Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
  [2024-12-10T13:23:01.739776Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-10T13:23:01.739776Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] [ERROR] [2024-12-10T13:23:01.714804Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [getAlignmentStats_generateStats_000] /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
  [2024-12-10T13:23:01.739824Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
  [2024-12-10T13:23:01.747691Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_001' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.001.xml --align-file test2.paired_end.recalibrated.sorted.cram'
  [2024-12-10T13:23:01.747740Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_001] Error Message:
  [2024-12-10T13:23:01.747757Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_001] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-10T13:23:01.747757Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] [ERROR] [2024-12-10T13:23:01.740945Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [getAlignmentStats_generateStats_001] /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
  [2024-12-10T13:23:01.798232Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Retrying task: 'getChromDepth_sample000_estimateChromDepth_000_chr21'. Total prior task failures: 2
  [2024-12-10T13:23:01.800680Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
  [2024-12-10T13:23:01.861955Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_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-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/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'
  [2024-12-10T13:23:01.862068Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Error Message:
  [2024-12-10T13:23:01.862091Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-10T13:23:01.862091Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [TaskManager] [ERROR] [2024-12-10T13:23:01.823477Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [getChromDepth_sample000_estimateChromDepth_000_chr21] /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
  [2024-12-10T13:23:04.698545Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
  [2024-12-10T13:23:04.698599Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_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-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
  [2024-12-10T13:23:04.698677Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
  [2024-12-10T13:23:04.698701Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-10T13:23:04.698701Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [WorkflowRunner] [ERROR] [2024-12-10T13:23:01.714804Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [getAlignmentStats_generateStats_000] /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
  [2024-12-10T13:23:04.698742Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_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-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/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'
  [2024-12-10T13:23:04.698782Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Error Message:
  [2024-12-10T13:23:04.698802Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-10T13:23:04.698802Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [WorkflowRunner] [ERROR] [2024-12-10T13:23:01.823477Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [getChromDepth_sample000_estimateChromDepth_000_chr21] /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
  [2024-12-10T13:23:04.698826Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_001' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.001.xml --align-file test2.paired_end.recalibrated.sorted.cram'
  [2024-12-10T13:23:04.698853Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_001] Error Message:
  [2024-12-10T13:23:04.698869Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_001] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-10T13:23:04.698869Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [WorkflowRunner] [ERROR] [2024-12-10T13:23:01.740945Z] [fv-az575-826.txkdwr3xd4ruhezurzmahy12zg.cx.internal.cloudapp.net] [131687_1] [getAlignmentStats_generateStats_001] /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats: 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/98/8dd4a2f5f0866317d5c63778714d74

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/d83ad9e6ce5149f25ccf62ff7c16f9a9/meta/nextflow.log' file for details
Join mismatch for the following entries: key=[id:sample4_vs_sample3, normal_id:sample3, patient:test3, sex:XX, tumor_id:sample4] values=


-[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