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Merge pull request #1755 from FriederikeHanssen/localmod #6952

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

9 tests run, 7 passed, 0 skipped, 2 failed.

Annotations

Check failure on line 1 in Test pipeline

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` [tiny_swartz] DSL2 - revision: 3954909713

-[2m----------------------------------------------------[0m-
                                        [0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m        ___     __   __   __   ___     [0;32m/,-._.--~'[0m
[0;34m  |\ | |__  __ /  ` /  \ |__) |__         [0;33m}  {[0m
[0;34m  | \| |       \__, \__/ |  \ |___     [0;32m\`-._,-`-,[0m
                                        [0;32m`._,._,'[0m
[0;37m      ____[0m
[0;37m    .´ _  `.[0m
[0;37m   /  [0;32m|\[0m`-_ \[0m     [0;34m __        __   ___     [0m
[0;37m  |   [0;32m| \[0m  `-|[0m    [0;34m|__`  /\  |__) |__  |__/[0m
[0;37m   \ [0;32m|   \[0m  /[0m     [0;34m.__| /¯¯\ |  \ |___ |  \[0m
[0;37m    `[0;32m|[0m____[0;32m\[0m´[0m

[0;35m  nf-core/sarek 3.5.0[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
  [0;34minput                     : [0;32m/home/runner/work/sarek/sarek/tests/csv/3.0/recalibrated_somatic.csv[0m
  [0;34mstep                      : [0;32mvariant_calling[0m
  [0;34moutdir                    : [0;32m/home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/output[0m

[1mMain options[0m
  [0;34msplit_fastq               : [0;32m0[0m
  [0;34mintervals                 : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed[0m
  [0;34mwes                       : [0;32mtrue[0m
  [0;34mtools                     : [0;32mcontrolfreec[0m

[1mAnnotation[0m
  [0;34mbcftools_annotations      : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz[0m
  [0;34mbcftools_annotations_tbi  : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi[0m
  [0;34mbcftools_header_lines     : [0;32m/home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt[0m

[1mGeneral reference genome options[0m
  [0;34migenomes_base             : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/[0m

[1mReference genome options[0m
  [0;34mgenome                    : [0;32mtestdata.nf-core.sarek[0m
  [0;34mchr_dir                   : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz[0m
  [0;34mdbsnp                     : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz[0m
  [0;34mdbsnp_tbi                 : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi[0m
  [0;34mdbsnp_vqsr                : [0;32m--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz[0m
  [0;34mdict                      : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict[0m
  [0;34mfasta                     : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta[0m
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  [0;34mknown_indels_tbi          : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi[0m
  [0;34mknown_indels_vqsr         : [0;32m--resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz[0m
  [0;34mngscheckmate_bed          : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed[0m
  [0;34msentieon_dnascope_model   : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model[0m
  [0;34msnpeff_cache              : [0;32mnull[0m
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  [0;34mvep_cache_version         : [0;32m113[0m
  [0;34mvep_genome                : [0;32mWBcel235[0m
  [0;34mvep_species               : [0;32mcaenorhabditis_elegans[0m

[1mInstitutional config options[0m
  [0;34mconfig_profile_name       : [0;32mTest profile[0m
  [0;34mconfig_profile_description: [0;32mMinimal test dataset to check pipeline function[0m
  [0;34mmodules_testdata_base_path: [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/[0m

[1mCore Nextflow options[0m
  [0;34mrunName                   : [0;32mtiny_swartz[0m
  [0;34mlaunchDir                 : [0;32m/home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32[0m
  [0;34mworkDir                   : [0;32m/home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work[0m
  [0;34mprojectDir                : [0;32m/home/runner/work/sarek/sarek[0m
  [0;34muserName                  : [0;32mrunner[0m
  [0;34mprofile                   : [0;32mtest,conda[0m
  [0;34mconfigFiles               : [0;32m[0m

!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* 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-47b5d3c40746bfdb673888286797637b]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-5a9ba0ebb7bcf86c-497b0f18c811c5671b5e17e0034188ed]
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/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/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/d46f6304d77366be7c2f91242287e32/work/conda/env-1abf3db016bf3fb9-873a3583ebab040412cb72c07ed757ab]
[31/c91989] 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]
[87/5bb95a] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[23/dd248e] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[81/70db2e] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[7b/1b7c60] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[b6/4e8f1e] Submitted process > NFCORE_SAREK:PREPARE_GENOME:UNTAR_CHR_DIR (chromosomes.tar.gz)
[ed/cd55cc] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)
[88/d5717e] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_2-23354000)
[fa/9d5562] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_TUMOR:SAMTOOLS_MPILEUP (sample4_vs_sample3)
[75/328b57] 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]
[d4/cfe80d] 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/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]
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/freec2bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/env-00cc74a07c8305aa-b045b606f9dcfe6897fe2c50e0f58bc7]
[f3/8229bf] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:FREEC2CIRCOS (sample4_vs_sample3)
[43/4316e9] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:FREEC2BED (sample4_vs_sample3)
[04/5400e3] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:MAKEGRAPH2 (sample4_vs_sample3)
[2f/192703] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC:ASSESS_SIGNIFICANCE (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]
[f8/d21ae8] Submitted process > NFCORE_SAREK:SAREK:MULTIQC
-[0;35m[nf-core/sarek][0;32m Pipeline completed successfully[0m-
Nextflow stderr:

Check failure on line 1 in Test pipeline

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` [furious_sax] DSL2 - revision: 3954909713

-[2m----------------------------------------------------[0m-
                                        [0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m        ___     __   __   __   ___     [0;32m/,-._.--~'[0m
[0;34m  |\ | |__  __ /  ` /  \ |__) |__         [0;33m}  {[0m
[0;34m  | \| |       \__, \__/ |  \ |___     [0;32m\`-._,-`-,[0m
                                        [0;32m`._,._,'[0m
[0;37m      ____[0m
[0;37m    .´ _  `.[0m
[0;37m   /  [0;32m|\[0m`-_ \[0m     [0;34m __        __   ___     [0m
[0;37m  |   [0;32m| \[0m  `-|[0m    [0;34m|__`  /\  |__) |__  |__/[0m
[0;37m   \ [0;32m|   \[0m  /[0m     [0;34m.__| /¯¯\ |  \ |___ |  \[0m
[0;37m    `[0;32m|[0m____[0;32m\[0m´[0m

[0;35m  nf-core/sarek 3.5.0[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
  [0;34minput                     : [0;32m/home/runner/work/sarek/sarek/tests/csv/3.0/recalibrated_somatic.csv[0m
  [0;34mstep                      : [0;32mvariant_calling[0m
  [0;34moutdir                    : [0;32m/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/output[0m

[1mMain options[0m
  [0;34msplit_fastq               : [0;32m0[0m
  [0;34mintervals                 : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed[0m
  [0;34mno_intervals              : [0;32mtrue[0m
  [0;34mtools                     : [0;32mmanta,strelka[0m

[1mAnnotation[0m
  [0;34mbcftools_annotations      : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz[0m
  [0;34mbcftools_annotations_tbi  : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi[0m
  [0;34mbcftools_header_lines     : [0;32m/home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt[0m

[1mGeneral reference genome options[0m
  [0;34migenomes_base             : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/[0m

[1mReference genome options[0m
  [0;34mgenome                    : [0;32mtestdata.nf-core.sarek[0m
  [0;34mdbsnp                     : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz[0m
  [0;34mdbsnp_tbi                 : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi[0m
  [0;34mdbsnp_vqsr                : [0;32m--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz[0m
  [0;34mdict                      : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict[0m
  [0;34mfasta                     : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta[0m
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  [0;34mknown_indels              : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz[0m
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  [0;34mknown_indels_vqsr         : [0;32m--resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz[0m
  [0;34mngscheckmate_bed          : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed[0m
  [0;34msentieon_dnascope_model   : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model[0m
  [0;34msnpeff_cache              : [0;32mnull[0m
  [0;34msnpeff_db                 : [0;32mWBcel235.105[0m
  [0;34mvep_cache                 : [0;32mnull[0m
  [0;34mvep_cache_version         : [0;32m113[0m
  [0;34mvep_genome                : [0;32mWBcel235[0m
  [0;34mvep_species               : [0;32mcaenorhabditis_elegans[0m

[1mInstitutional config options[0m
  [0;34mconfig_profile_name       : [0;32mTest profile[0m
  [0;34mconfig_profile_description: [0;32mMinimal test dataset to check pipeline function[0m
  [0;34mmodules_testdata_base_path: [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/[0m

[1mCore Nextflow options[0m
  [0;34mrunName                   : [0;32mfurious_sax[0m
  [0;34mlaunchDir                 : [0;32m/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9[0m
  [0;34mworkDir                   : [0;32m/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work[0m
  [0;34mprojectDir                : [0;32m/home/runner/work/sarek/sarek[0m
  [0;34muserName                  : [0;32mrunner[0m
  [0;34mprofile                   : [0;32mtest,conda[0m
  [0;34mconfigFiles               : [0;32m[0m

!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* 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/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_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/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/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_germline_manta/../../../modules/nf-core/manta/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f]
[06/9a9fda] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (no_intervals)
[e5/c31de0] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
[1e/ed467e] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[e5/c31de0] 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)
[1d/8502b0] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[99/c9412d] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[a8/0a53e9] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[e4/93ba40] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
[e4/93ba40] 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)
[40/a3193b] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (sample3)
[dd/cd0c78] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (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]
[dd/cd0c78] 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)
[7b/14aaf2] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
[7b/14aaf2] 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)
[89/aeeb39] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample3)
[f5/ecb375] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample3)
[b5/709572] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample3)
[84/25fc57] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample3)
[21/71dfe8] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
[73/efdffd] 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:
  [2024-12-11T18:25:05.438508Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] Adding command task 'tabix_sortCandidateSV' to master workflow
  [2024-12-11T18:25:05.439273Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortDiploidSV' to master workflow
  [2024-12-11T18:25:05.439562Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] Adding sub-workflow task 'sortDiploidSVInputList' to master workflow
  [2024-12-11T18:25:05.439813Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] Adding command task 'sort_sortDiploidSV' to master workflow
  [2024-12-11T18:25:05.440012Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] Adding command task 'tabix_sortDiploidSV' to master workflow
  [2024-12-11T18:25:05.440242Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] Adding command task 'extractSmallIndels' to master workflow
  [2024-12-11T18:25:05.441077Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] Adding command task 'extractSmallIndels_tabix' to master workflow
  [2024-12-11T18:25:05.441382Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] Adding sub-workflow task 'sortEdgeRuntimeLogsInputList' to master workflow
  [2024-12-11T18:25:05.441622Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] Adding command task 'sortEdgeRuntimeLogs' to master workflow
  [2024-12-11T18:25:05.441758Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
  [2024-12-11T18:25:05.441919Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getChromDepth_makeTmpDir] Task initiated on local node
  [2024-12-11T18:25:05.474168Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] Completed command task: 'getAlignmentStats_makeTmpDir' launched from master workflow
  [2024-12-11T18:25:05.474246Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] Completed command task: 'getChromDepth_makeTmpDir' launched from master workflow
  [2024-12-11T18:25:05.474833Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] Launching command task: 'getChromDepth_sample000_makeTmpDir' from master workflow
  [2024-12-11T18:25:05.475064Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_000' from master workflow
  [2024-12-11T18:25:05.478068Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getChromDepth_sample000_makeTmpDir] Task initiated on local node
  [2024-12-11T18:25:05.478777Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
  [2024-12-11T18:25:05.505171Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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'
  [2024-12-11T18:25:05.507030Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] Completed command task: 'getChromDepth_sample000_makeTmpDir' launched from master workflow
  [2024-12-11T18:25:05.507561Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] Launching command task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' from master workflow
  [2024-12-11T18:25:05.509788Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
  [2024-12-11T18:25:05.535902Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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'
  [2024-12-11T18:26:35.579489Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getAlignmentStats_generateStats_000] Retrying task: 'getAlignmentStats_generateStats_000'. Total prior task failures: 1
  [2024-12-11T18:26:35.581894Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
  [2024-12-11T18:26:35.608589Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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'
  [2024-12-11T18:26:35.622407Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Retrying task: 'getChromDepth_sample000_estimateChromDepth_000_chr21'. Total prior task failures: 1
  [2024-12-11T18:26:35.624439Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
  [2024-12-11T18:26:35.650500Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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'
  [2024-12-11T18:28:05.674384Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getAlignmentStats_generateStats_000] Retrying task: 'getAlignmentStats_generateStats_000'. Total prior task failures: 2
  [2024-12-11T18:28:05.676739Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
  [2024-12-11T18:28:05.738503Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Retrying task: 'getChromDepth_sample000_estimateChromDepth_000_chr21'. Total prior task failures: 2
  [2024-12-11T18:28:05.740811Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
  [2024-12-11T18:28:05.745086Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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'
  [2024-12-11T18:28:05.745515Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
  [2024-12-11T18:28:05.745591Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-11T18:28:05.745591Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] [ERROR] [2024-12-11T18:28:05.699259Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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
  [2024-12-11T18:28:05.745655Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
  [2024-12-11T18:28:05.777603Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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'
  [2024-12-11T18:28:05.777669Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Error Message:
  [2024-12-11T18:28:05.777700Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-11T18:28:05.777700Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [TaskManager] [ERROR] [2024-12-11T18:28:05.763270Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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
  [2024-12-11T18:28:08.697879Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
  [2024-12-11T18:28:08.697932Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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'
  [2024-12-11T18:28:08.697983Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Error Message:
  [2024-12-11T18:28:08.698007Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-11T18:28:08.698007Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] [ERROR] [2024-12-11T18:28:05.763270Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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
  [2024-12-11T18:28:08.698042Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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'
  [2024-12-11T18:28:08.698082Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
  [2024-12-11T18:28:08.698105Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Last 1 stderr lines from task (of 1 total lines):
  [2024-12-11T18:28:08.698105Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_1] [WorkflowRunner] [ERROR] [2024-12-11T18:28:05.699259Z] [fv-az1776-349.vx1cfmhndxiupj3i50m0fbu2we.cx.internal.cloudapp.net] [131727_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

Work dir:
  /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/21/71dfe8716bc1f11d1f974153b9b407

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- 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
-[0;35m[nf-core/sarek][0;31m Pipeline completed with errors[0m-
WARN: Killing running tasks (1)
Nextflow stderr:

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