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Merge pull request #1754 from FriederikeHanssen/fixtest #6626

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

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

Annotations

Check failure on line 1 in Test pipeline

github-actions / JUnit Test Report

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

Assertion failed: 

2 of 2 assertions failed

Raw output


            Nextflow stdout:

N E X T F L O W  ~  version 24.04.2
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [compassionate_kalam] 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/fastq_pair.csv[0m
  [0;34moutdir                    : [0;32m/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/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/genome.interval_list[0m
  [0;34mtools                     : [0;32mstrelka[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/genome.fasta[0m
  [0;34mfasta_fai                 : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.fasta.fai[0m
  [0;34mgermline_resource         : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz[0m
  [0;34mgermline_resource_tbi     : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi[0m
  [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
  [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
  [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;32mcompassionate_kalam[0m
  [0;34mlaunchDir                 : [0;32m/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0[0m
  [0;34mworkDir                   : [0;32m/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/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

WARN: FASTQ file(/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz): Cannot extract flowcell ID from @normal#21#998579#1/1
WARN: FASTQ file(/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz): Cannot extract flowcell ID from @normal#21#998513#1/1
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/bwa/index/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-b7d45abbc59134ec734c2810969e7f00]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/gawk-f9b4f646bf1b67e52890543d27cb2f27]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/gatk4/intervallisttobed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-d2d82a1cc7858810940ff84273e57b63]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/fastqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-3ea42529974ca5a54ae5623eacfbc76a]
[be/1f13e9] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (genome.interval_list)
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-497b0f18c811c5671b5e17e0034188ed]
[f9/b25aae] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test-test_L1)
[62/de7abb] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test2-test_L1)
[37/bd5de3] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED (genome)
[0f/be4671] Submitted process > NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX (genome.fasta)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/../../../modules/nf-core/bwa/mem/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-302c740918ed3eabd6af342133129057]
[8e/4a4892] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr22_1-40001)
[c3/938b7f] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (genome)
[c1/b6c219] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test)
[ed/ccd9ef] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test2)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../../../modules/nf-core/gatk4/markduplicates/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-7753f12b1b6af37c6e7eb5fd03e42240]
[99/bd04d8] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (test2)
[fb/c9d1d6] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-873a3583ebab040412cb72c07ed757ab]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-57cd7e91fe23a8ceb488416c37dae89b]
[e5/f6a671] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test2)
[e8/04854d] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test2)
[a2/4c737b] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test)
[c5/13ce72] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test)
[e0/c56cc5] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test2)
[e4/5cb902] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test)
[cf/574ac2] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test2)
[f7/dd947c] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (test2)
[ea/428e8b] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (test2)
[8a/df4a20] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (test)
[8b/4d3ff8] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (test2)
[c2/71f7e8] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test)
[1b/ed1247] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_single_strelka/../../../modules/nf-core/strelka/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce]
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (1)'

Caused by:
  java.nio.channels.OverlappingFileLockException



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

 -- Check '/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/meta/nextflow.log' file for details
-[0;35m[nf-core/sarek][0;31m Pipeline completed with errors[0m-
WARN: Killing running tasks (1)
Nextflow stderr:

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

Check failure on line 1 in Test pipeline

github-actions / JUnit Test Report

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

Assertion failed: 

2 of 2 assertions failed

Raw output


            Nextflow stdout:

N E X T F L O W  ~  version 24.04.2
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [loquacious_lavoisier] 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.csv[0m
  [0;34mstep                       : [0;32mvariant_calling[0m
  [0;34moutdir                     : [0;32m/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/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;34mtools                      : [0;32mstrelka[0m

[1mVariant Calling[0m
  [0;34monly_paired_variant_calling: [0;32mtrue[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
  [0;34mfasta_fai                  : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai[0m
  [0;34mgermline_resource          : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz[0m
  [0;34mgermline_resource_tbi      : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi[0m
  [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
  [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
  [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;32mloquacious_lavoisier[0m
  [0;34mlaunchDir                  : [0;32m/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132[0m
  [0;34mworkDir                    : [0;32m/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/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/fa9ac3ed693ca54cacee2f6c2755132/work/conda/environment-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/fa9ac3ed693ca54cacee2f6c2755132/work/conda/gawk-f9b4f646bf1b67e52890543d27cb2f27]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/environment-57cd7e91fe23a8ceb488416c37dae89b]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/environment-873a3583ebab040412cb72c07ed757ab]
[e5/d4c535] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)
[61/003817] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[ab/e88b7a] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample2)
[dc/fbefd8] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[ee/0c319c] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample1)
[e7/f1ffd4] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[cc/cabe50] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample1)
[1e/7c20c1] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample2)
[94/071fe1] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[2c/6f83b0] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[19/9b8026] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_2-23354000)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_strelka/../../../modules/nf-core/strelka/somatic/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce]
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (1)'

Caused by:
  java.nio.channels.OverlappingFileLockException



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

 -- Check '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/meta/nextflow.log' file for details
-[0;35m[nf-core/sarek][0;31m Pipeline completed with errors[0m-
Nextflow stderr:

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

Check failure on line 1 in Test pipeline

github-actions / JUnit Test Report

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

Assertion failed: 

2 of 2 assertions failed

Raw output


            Nextflow stdout:

N E X T F L O W  ~  version 24.04.2
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [clever_roentgen] 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/7bf95e035d07a296db4135640ce7bd60/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;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
  [0;34mfasta_fai                 : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai[0m
  [0;34mgermline_resource         : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz[0m
  [0;34mgermline_resource_tbi     : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi[0m
  [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
  [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
  [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;32mclever_roentgen[0m
  [0;34mlaunchDir                 : [0;32m/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60[0m
  [0;34mworkDir                   : [0;32m/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/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/7bf95e035d07a296db4135640ce7bd60/work/conda/gawk-f9b4f646bf1b67e52890543d27cb2f27]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-497b0f18c811c5671b5e17e0034188ed]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-873a3583ebab040412cb72c07ed757ab]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-57cd7e91fe23a8ceb488416c37dae89b]
[95/b7c5ca] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[ce/1f019b] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[3c/d847b8] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[9f/190095] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[1b/bc3e76] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[f5/44498c] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_2-23354000)
[ee/538bb5] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_single_strelka/../../../modules/nf-core/strelka/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-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/7bf95e035d07a296db4135640ce7bd60/work/conda/environment-86f8fc4b934d0b08515f88ef4592bd1f]
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (1)'

Caused by:
  java.nio.channels.OverlappingFileLockException



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

 -- Check '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/meta/nextflow.log' file for details
-[0;35m[nf-core/sarek][0;31m Pipeline completed with errors[0m-
Join mismatch for the following entries: key=[id:sample4_vs_sample3, normal_id:sample3, patient:test3, sex:XX, tumor_id:sample4] values=


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

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

View more details on GitHub Actions