Merge pull request #1613 from lindenb/pl_goleft #6940
GitHub Actions / JUnit Test Report
failed
Dec 10, 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 24.11.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [cheeky_aryabhata] DSL2 - revision: 3954909713
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[0;32m,--.[0;30m/[0;32m,-.[0m
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[0;32m`._,._,'[0m
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[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;32mcheeky_aryabhata[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_intervals/../../../modules/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-b45f4430b1ab9d6e-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/env-73143911187759b2-d2d82a1cc7858810940ff84273e57b63]
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/env-5f8479c2edf694ea-b7d45abbc59134ec734c2810969e7f00]
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/env-d3cbe95ac01651f4-3ea42529974ca5a54ae5623eacfbc76a]
[4e/07c807] 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/env-5a9ba0ebb7bcf86c-497b0f18c811c5671b5e17e0034188ed]
[34/79b791] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test-test_L1)
[3c/9e2c33] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test2-test_L1)
[06/e1bab9] 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/env-ebc35d8fd1c430d4-302c740918ed3eabd6af342133129057]
[56/617122] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED (genome)
[cc/2991b0] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test)
[7c/0adc17] 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/env-2421a9d4f9dcd0b1-7753f12b1b6af37c6e7eb5fd03e42240]
[c6/0dbc92] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (genome)
[38/5e6d7e] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr22_1-40001)
[33/93e5a4] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (test)
[69/a6eff8] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (test2)
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/env-1abf3db016bf3fb9-873a3583ebab040412cb72c07ed757ab]
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/env-c5b497d07713b814-57cd7e91fe23a8ceb488416c37dae89b]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_baserecalibrator/../../../modules/nf-core/gatk4/baserecalibrator/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-7d2dddae736a8a74-d2d82a1cc7858810940ff84273e57b63]
[45/8b3e87] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test)
[04/271fb8] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test2)
[0d/303a92] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test)
[58/f0327b] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test2)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_applybqsr/../../../modules/nf-core/gatk4/applybqsr/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-0da3f2d475a1f2b8-d2d82a1cc7858810940ff84273e57b63]
[dc/15dbf2] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (test2)
[96/9d9609] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (test)
[d4/8496b0] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test2)
[bd/07e4f4] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_applybqsr/../cram_merge_index_samtools/../../../modules/nf-core/samtools/index/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-bc98654c03cc37f5-873a3583ebab040412cb72c07ed757ab]
[81/5022e2] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test)
[fb/3dac0c] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test2)
[3b/580b27] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (test2)
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/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_single_strelka/../../../modules/nf-core/strelka/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-90ad7ffecab6b5bf-438a505d7b44a08705c858f9ad6e02ce]
[26/6dfc25] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (test)
[b1/01f985] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (test2)
[2b/14c1de] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (test)
[10/a1484a] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)
[61/78ddff] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)
[10/a1484a] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)` terminated with an error exit status (1) -- Execution is retried (1)
[61/78ddff] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)` terminated with an error exit status (1) -- Execution is retried (2)
[ee/f63b43] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (test)
[c2/886c89] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)
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/14ed1c6de97f743ae4153d1d9e2a1f0/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/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-ac437bb99679f3c6-ede778c78582be405557f3c8ca0e9927]
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)'
Caused by:
Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)` terminated with an error exit status (1)
Command executed:
configureStrelkaSomaticWorkflow.py \
--tumor test2.recal.cram \
--normal test.recal.cram \
--referenceFasta genome.fasta \
--callRegions chr22_1-40001.bed.gz \
\
\
--runDir strelka
sed -i s/"isEmail = isLocalSmtp()"/"isEmail = False"/g strelka/runWorkflow.py
python strelka/runWorkflow.py -m local -j 4
mv strelka/results/variants/somatic.indels.vcf.gz test2_vs_test.strelka.somatic_indels.vcf.gz
mv strelka/results/variants/somatic.indels.vcf.gz.tbi test2_vs_test.strelka.somatic_indels.vcf.gz.tbi
mv strelka/results/variants/somatic.snvs.vcf.gz test2_vs_test.strelka.somatic_snvs.vcf.gz
mv strelka/results/variants/somatic.snvs.vcf.gz.tbi test2_vs_test.strelka.somatic_snvs.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC":
strelka: $( configureStrelkaSomaticWorkflow.py --version )
END_VERSIONS
Command exit status:
1
Command output:
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:
strelka/runWorkflow.py
Command error:
[2024-12-10T17:39:36.284177Z] [fv-az525-427] [125113_1] [TaskManager] Launching command task: 'getChromDepth_sample000_catChromDepth' from master workflow
[2024-12-10T17:39:36.286994Z] [fv-az525-427] [125113_1] [TaskRunner:getChromDepth_sample000_catChromDepth] Task initiated on local node
[2024-12-10T17:39:36.348430Z] [fv-az525-427] [125113_1] [TaskManager] Completed command task: 'getChromDepth_sample000_catChromDepth' launched from master workflow
[2024-12-10T17:39:36.348788Z] [fv-az525-427] [125113_1] [TaskManager] Launching command task: 'getChromDepth_mergeChromDepth' from master workflow
[2024-12-10T17:39:36.351459Z] [fv-az525-427] [125113_1] [TaskRunner:getChromDepth_mergeChromDepth] Task initiated on local node
[2024-12-10T17:39:36.412879Z] [fv-az525-427] [125113_1] [TaskManager] Completed command task: 'getChromDepth_mergeChromDepth' launched from master workflow
[2024-12-10T17:39:36.413307Z] [fv-az525-427] [125113_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2024-12-10T17:39:36.413468Z] [fv-az525-427] [125113_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2024-12-10T17:39:36.413993Z] [fv-az525-427] [125113_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2024-12-10T17:39:36.414439Z] [fv-az525-427] [125113_1] [TaskManager] Launching command task: 'getChromDepth_removeTmpDir' from master workflow
[2024-12-10T17:39:36.414809Z] [fv-az525-427] [125113_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
[2024-12-10T17:39:36.415646Z] [fv-az525-427] [125113_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
[2024-12-10T17:39:36.416540Z] [fv-az525-427] [125113_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
[2024-12-10T17:39:36.418210Z] [fv-az525-427] [125113_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2024-12-10T17:39:36.419153Z] [fv-az525-427] [125113_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2024-12-10T17:39:36.419814Z] [fv-az525-427] [125113_1] [TaskRunner:getChromDepth_removeTmpDir] Task initiated on local node
[2024-12-10T17:39:36.420190Z] [fv-az525-427] [125113_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2024-12-10T17:39:36.420798Z] [fv-az525-427] [125113_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2024-12-10T17:39:36.421175Z] [fv-az525-427] [125113_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2024-12-10T17:39:36.423552Z] [fv-az525-427] [125113_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2024-12-10T17:39:36.423891Z] [fv-az525-427] [125113_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2024-12-10T17:39:36.424168Z] [fv-az525-427] [125113_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2024-12-10T17:39:36.424718Z] [fv-az525-427] [125113_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2024-12-10T17:39:36.425038Z] [fv-az525-427] [125113_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2024-12-10T17:39:36.457531Z] [fv-az525-427] [125113_1] [TaskManager] Completed command task: 'getChromDepth_removeTmpDir' launched from master workflow
[2024-12-10T17:39:36.465210Z] [fv-az525-427] [125113_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2024-12-10T17:39:36.465546Z] [fv-az525-427] [125113_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' from sub-workflow 'CallGenome'
[2024-12-10T17:39:36.468069Z] [fv-az525-427] [125113_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_000_chr22_0000] Task initiated on local node
[2024-12-10T17:39:36.629798Z] [fv-az525-427] [125113_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr22:1-40001 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr22_1-40001.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.recal.cram --tumor-align-file test2.recal.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr22_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr22_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr22_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-10T17:39:36.629931Z] [fv-az525-427] [125113_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Error Message:
[2024-12-10T17:39:36.629955Z] [fv-az525-427] [125113_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
[2024-12-10T17:39:36.629978Z] [fv-az525-427] [125113_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Logging 5 line(s) of task wrapper log output below:
[2024-12-10T17:39:36.630003Z] [fv-az525-427] [125113_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-10T17:39:36.483916Z] [fv-az525-427] [125113_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] wrapperStart
[2024-12-10T17:39:36.630037Z] [fv-az525-427] [125113_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-10T17:39:36.489795Z] [fv-az525-427] [125113_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStart
[2024-12-10T17:39:36.630067Z] [fv-az525-427] [125113_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-10T17:39:36.588524Z] [fv-az525-427] [125113_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskExitCode -11
[2024-12-10T17:39:36.630093Z] [fv-az525-427] [125113_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-10T17:39:36.589674Z] [fv-az525-427] [125113_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStderrTail 1
[2024-12-10T17:39:36.630115Z] [fv-az525-427] [125113_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-10T17:39:36.630140Z] [fv-az525-427] [125113_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
[2024-12-10T17:39:37.445789Z] [fv-az525-427] [125113_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2024-12-10T17:39:38.763268Z] [fv-az525-427] [125113_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2024-12-10T17:39:38.763306Z] [fv-az525-427] [125113_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr22:1-40001 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr22_1-40001.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.recal.cram --tumor-align-file test2.recal.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr22_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr22_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr22_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-10T17:39:38.763341Z] [fv-az525-427] [125113_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Error Message:
[2024-12-10T17:39:38.763355Z] [fv-az525-427] [125113_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
[2024-12-10T17:39:38.763369Z] [fv-az525-427] [125113_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Logging 5 line(s) of task wrapper log output below:
[2024-12-10T17:39:38.763382Z] [fv-az525-427] [125113_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-10T17:39:36.483916Z] [fv-az525-427] [125113_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] wrapperStart
[2024-12-10T17:39:38.763398Z] [fv-az525-427] [125113_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-10T17:39:36.489795Z] [fv-az525-427] [125113_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStart
[2024-12-10T17:39:38.763411Z] [fv-az525-427] [125113_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-10T17:39:36.588524Z] [fv-az525-427] [125113_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskExitCode -11
[2024-12-10T17:39:38.763424Z] [fv-az525-427] [125113_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-10T17:39:36.589674Z] [fv-az525-427] [125113_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStderrTail 1
[2024-12-10T17:39:38.763440Z] [fv-az525-427] [125113_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-10T17:39:38.763453Z] [fv-az525-427] [125113_1] [WorkflowRunner] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
Work dir:
/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/c2/886c89b9e42766c2d265721d35c217
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '/home/runner/work/sarek/sarek/~/tests/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-
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/multiqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-7da4088df3b01749-eec4e05336245ea50db6412788f8c4da]
Nextflow stderr:
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 24.11.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [sad_lamport] DSL2 - revision: 3954909713
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
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[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;32msad_lamport[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/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-b45f4430b1ab9d6e-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/fa9ac3ed693ca54cacee2f6c2755132/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/fa9ac3ed693ca54cacee2f6c2755132/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/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-c5b497d07713b814-57cd7e91fe23a8ceb488416c37dae89b]
[f3/ef9f8d] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[ed/ef8356] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample1)
[bd/afd482] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[5c/036502] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[85/2d7037] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample2)
[e9/b78c7c] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample2)
[24/c7bbfa] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample1)
[c5/0e0679] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_2-23354000)
[d2/75c4b1] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)
[1b/927fb0] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
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/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_single_strelka/../../../modules/nf-core/strelka/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-90ad7ffecab6b5bf-438a505d7b44a08705c858f9ad6e02ce]
[a4/a66fa8] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[86/fcd284] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)
[fc/258d12] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (sample1)
[86/fcd284] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1) -- Execution is retried (1)
[28/99c114] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_qc_bcftools_vcftools/../../../modules/nf-core/bcftools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/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/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-ac437bb99679f3c6-ede778c78582be405557f3c8ca0e9927]
[28/99c114] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1) -- Execution is retried (2)
[5c/0b4d0c] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)'
Caused by:
Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1)
Command executed:
configureStrelkaSomaticWorkflow.py \
--tumor test2.paired_end.recalibrated.sorted.cram \
--normal test.paired_end.recalibrated.sorted.cram \
--referenceFasta genome.fasta \
--callRegions chr21_2-23354000.bed.gz \
\
\
--runDir strelka
sed -i s/"isEmail = isLocalSmtp()"/"isEmail = False"/g strelka/runWorkflow.py
python strelka/runWorkflow.py -m local -j 4
mv strelka/results/variants/somatic.indels.vcf.gz sample4_vs_sample3.strelka.somatic_indels.vcf.gz
mv strelka/results/variants/somatic.indels.vcf.gz.tbi sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
mv strelka/results/variants/somatic.snvs.vcf.gz sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
mv strelka/results/variants/somatic.snvs.vcf.gz.tbi sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC":
strelka: $( configureStrelkaSomaticWorkflow.py --version )
END_VERSIONS
Command exit status:
1
Command output:
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:
strelka/runWorkflow.py
Command error:
[2024-12-10T17:41:44.893603Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-10T17:41:44.844819Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStderrTail 1
[2024-12-10T17:41:44.893623Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-10T17:41:44.909540Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0001' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:11677497-23354992 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0001.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0001.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0001.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-10T17:41:44.909638Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Error Message:
[2024-12-10T17:41:44.909663Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/011/pyflowTaskWrapper.signal.txt'
[2024-12-10T17:41:44.909686Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Logging 5 line(s) of task wrapper log output below:
[2024-12-10T17:41:44.909706Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-10T17:41:44.711166Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] wrapperStart
[2024-12-10T17:41:44.909724Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-10T17:41:44.722871Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStart
[2024-12-10T17:41:44.909745Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-10T17:41:44.897128Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskExitCode -11
[2024-12-10T17:41:44.909771Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-10T17:41:44.898158Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStderrTail 1
[2024-12-10T17:41:44.909790Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-10T17:41:45.574858Z] [fv-az525-427] [130743_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2024-12-10T17:41:48.094167Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2024-12-10T17:41:48.094227Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0001' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:11677497-23354992 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0001.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0001.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0001.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-10T17:41:48.094282Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Error Message:
[2024-12-10T17:41:48.094306Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/011/pyflowTaskWrapper.signal.txt'
[2024-12-10T17:41:48.094338Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Logging 5 line(s) of task wrapper log output below:
[2024-12-10T17:41:48.094365Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-10T17:41:44.711166Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] wrapperStart
[2024-12-10T17:41:48.094399Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-10T17:41:44.722871Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStart
[2024-12-10T17:41:48.094425Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-10T17:41:44.897128Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskExitCode -11
[2024-12-10T17:41:48.094452Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-10T17:41:44.898158Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStderrTail 1
[2024-12-10T17:41:48.094479Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-10T17:41:48.094506Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0003' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:35032489-46709983 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0003.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0003.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0003.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-10T17:41:48.094552Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Error Message:
[2024-12-10T17:41:48.094574Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/015/pyflowTaskWrapper.signal.txt'
[2024-12-10T17:41:48.094598Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Logging 5 line(s) of task wrapper log output below:
[2024-12-10T17:41:48.094624Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-10T17:41:44.695111Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] wrapperStart
[2024-12-10T17:41:48.094650Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-10T17:41:44.704026Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStart
[2024-12-10T17:41:48.094677Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-10T17:41:44.843829Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskExitCode -11
[2024-12-10T17:41:48.094707Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-10T17:41:44.844819Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStderrTail 1
[2024-12-10T17:41:48.094734Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-10T17:41:48.094761Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2024-12-10T17:41:48.094787Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:1-11677496 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-10T17:41:48.094829Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Error Message:
[2024-12-10T17:41:48.094855Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
[2024-12-10T17:41:48.094890Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Logging 5 line(s) of task wrapper log output below:
[2024-12-10T17:41:48.094912Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2024-12-10T17:41:44.696827Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] wrapperStart
[2024-12-10T17:41:48.094937Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2024-12-10T17:41:44.712193Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStart
[2024-12-10T17:41:48.094965Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2024-12-10T17:41:44.865127Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskExitCode -11
[2024-12-10T17:41:48.094992Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2024-12-10T17:41:44.866215Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStderrTail 1
[2024-12-10T17:41:48.095019Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-10T17:41:48.095045Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0002' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:23354993-35032488 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0002.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0002.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0002.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-10T17:41:48.095092Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Error Message:
[2024-12-10T17:41:48.095114Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/013/pyflowTaskWrapper.signal.txt'
[2024-12-10T17:41:48.095143Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Logging 5 line(s) of task wrapper log output below:
[2024-12-10T17:41:48.095169Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2024-12-10T17:41:44.709530Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] wrapperStart
[2024-12-10T17:41:48.095194Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2024-12-10T17:41:44.718007Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskStart
[2024-12-10T17:41:48.095222Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2024-12-10T17:41:44.882118Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskExitCode -11
[2024-12-10T17:41:48.095248Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2024-12-10T17:41:44.883138Z] [fv-az525-427] [130743_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskStderrTail 1
[2024-12-10T17:41:48.095281Z] [fv-az525-427] [130743_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
Work dir:
/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/5c/0b4d0c485cecd3bc65c792ecf6e03e
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/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-
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/multiqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-7da4088df3b01749-eec4e05336245ea50db6412788f8c4da]
Nextflow stderr:
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 24.11.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [naughty_franklin] DSL2 - revision: 3954909713
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
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[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;37m ____[0m
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[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
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[0;34mlaunchDir : [0;32m/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60[0m
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[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/env-b45f4430b1ab9d6e-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/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/7bf95e035d07a296db4135640ce7bd60/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/7bf95e035d07a296db4135640ce7bd60/work/conda/env-c5b497d07713b814-57cd7e91fe23a8ceb488416c37dae89b]
[bb/f2e464] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[dc/3e0978] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[b6/70343d] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[38/3091b3] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[f6/48cfcf] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[7c/9e1f95] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_2-23354000)
[55/caa198] 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_germline_manta/../../../modules/nf-core/manta/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-30739cc20e367bec-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/7bf95e035d07a296db4135640ce7bd60/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/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f]
[ac/9e6e75] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
[c2/7d2e74] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
[ac/9e6e75] 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)
[c2/7d2e74] 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)
[46/476f3f] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (sample3)
[48/5ac2a0] 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/bcftools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/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/7bf95e035d07a296db4135640ce7bd60/work/conda/env-ac437bb99679f3c6-ede778c78582be405557f3c8ca0e9927]
[48/5ac2a0] 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)
[cf/892d88] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
[cf/892d88] 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)
[6d/7741ba] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample3)
[cf/565442] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample3)
[0c/898f0c] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample3)
[b0/55c9b6] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample3)
[a5/9c22fc] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
[2b/77f402] 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 \
--callRegions multi_intervals.bed.gz \
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:
[2024-12-10T17:55:55.435514Z] [fv-az525-427] [145627_1] [WorkflowRunner] Adding command task 'sort_sortCandidateSV' to master workflow
[2024-12-10T17:55:55.435694Z] [fv-az525-427] [145627_1] [WorkflowRunner] Adding command task 'tabix_sortCandidateSV' to master workflow
[2024-12-10T17:55:55.435886Z] [fv-az525-427] [145627_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortDiploidSV' to master workflow
[2024-12-10T17:55:55.436333Z] [fv-az525-427] [145627_1] [WorkflowRunner] Adding sub-workflow task 'sortDiploidSVInputList' to master workflow
[2024-12-10T17:55:55.437304Z] [fv-az525-427] [145627_1] [WorkflowRunner] Adding command task 'sort_sortDiploidSV' to master workflow
[2024-12-10T17:55:55.437511Z] [fv-az525-427] [145627_1] [WorkflowRunner] Adding command task 'tabix_sortDiploidSV' to master workflow
[2024-12-10T17:55:55.437736Z] [fv-az525-427] [145627_1] [WorkflowRunner] Adding command task 'extractSmallIndels' to master workflow
[2024-12-10T17:55:55.437937Z] [fv-az525-427] [145627_1] [WorkflowRunner] Adding command task 'extractSmallIndels_tabix' to master workflow
[2024-12-10T17:55:55.438218Z] [fv-az525-427] [145627_1] [WorkflowRunner] Adding sub-workflow task 'sortEdgeRuntimeLogsInputList' to master workflow
[2024-12-10T17:55:55.438467Z] [fv-az525-427] [145627_1] [WorkflowRunner] Adding command task 'sortEdgeRuntimeLogs' to master workflow
[2024-12-10T17:55:55.438687Z] [fv-az525-427] [145627_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2024-12-10T17:55:55.470988Z] [fv-az525-427] [145627_1] [TaskManager] Completed command task: 'getAlignmentStats_makeTmpDir' launched from master workflow
[2024-12-10T17:55:55.471064Z] [fv-az525-427] [145627_1] [TaskManager] Completed command task: 'getChromDepth_makeTmpDir' launched from master workflow
[2024-12-10T17:55:55.471659Z] [fv-az525-427] [145627_1] [TaskManager] Launching command task: 'getChromDepth_sample000_makeTmpDir' from master workflow
[2024-12-10T17:55:55.471947Z] [fv-az525-427] [145627_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_000' from master workflow
[2024-12-10T17:55:55.474976Z] [fv-az525-427] [145627_1] [TaskRunner:getChromDepth_sample000_makeTmpDir] Task initiated on local node
[2024-12-10T17:55:55.475522Z] [fv-az525-427] [145627_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2024-12-10T17:55:55.506397Z] [fv-az525-427] [145627_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/7bf95e035d07a296db4135640ce7bd60/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'
[2024-12-10T17:55:55.535874Z] [fv-az525-427] [145627_1] [TaskManager] Completed command task: 'getChromDepth_sample000_makeTmpDir' launched from master workflow
[2024-12-10T17:55:55.536534Z] [fv-az525-427] [145627_1] [TaskManager] Launching command task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' from master workflow
[2024-12-10T17:55:55.539034Z] [fv-az525-427] [145627_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
[2024-12-10T17:55:55.569777Z] [fv-az525-427] [145627_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/7bf95e035d07a296db4135640ce7bd60/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'
[2024-12-10T17:57:25.543535Z] [fv-az525-427] [145627_1] [TaskRunner:getAlignmentStats_generateStats_000] Retrying task: 'getAlignmentStats_generateStats_000'. Total prior task failures: 1
[2024-12-10T17:57:25.545919Z] [fv-az525-427] [145627_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2024-12-10T17:57:25.573270Z] [fv-az525-427] [145627_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/7bf95e035d07a296db4135640ce7bd60/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'
[2024-12-10T17:57:25.652524Z] [fv-az525-427] [145627_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Retrying task: 'getChromDepth_sample000_estimateChromDepth_000_chr21'. Total prior task failures: 1
[2024-12-10T17:57:25.654753Z] [fv-az525-427] [145627_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
[2024-12-10T17:57:25.682007Z] [fv-az525-427] [145627_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/7bf95e035d07a296db4135640ce7bd60/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'
[2024-12-10T17:58:55.663280Z] [fv-az525-427] [145627_1] [TaskRunner:getAlignmentStats_generateStats_000] Retrying task: 'getAlignmentStats_generateStats_000'. Total prior task failures: 2
[2024-12-10T17:58:55.665779Z] [fv-az525-427] [145627_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2024-12-10T17:58:55.723570Z] [fv-az525-427] [145627_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/7bf95e035d07a296db4135640ce7bd60/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'
[2024-12-10T17:58:55.723694Z] [fv-az525-427] [145627_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2024-12-10T17:58:55.723718Z] [fv-az525-427] [145627_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 1 stderr lines from task (of 1 total lines):
[2024-12-10T17:58:55.723718Z] [fv-az525-427] [145627_1] [TaskManager] [ERROR] [2024-12-10T17:58:55.689201Z] [fv-az525-427] [145627_1] [getAlignmentStats_generateStats_000] /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/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
[2024-12-10T17:58:55.723882Z] [fv-az525-427] [145627_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
[2024-12-10T17:58:55.749236Z] [fv-az525-427] [145627_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Retrying task: 'getChromDepth_sample000_estimateChromDepth_000_chr21'. Total prior task failures: 2
[2024-12-10T17:58:55.751633Z] [fv-az525-427] [145627_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
[2024-12-10T17:58:55.788366Z] [fv-az525-427] [145627_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/7bf95e035d07a296db4135640ce7bd60/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'
[2024-12-10T17:58:55.788438Z] [fv-az525-427] [145627_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Error Message:
[2024-12-10T17:58:55.788462Z] [fv-az525-427] [145627_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Last 1 stderr lines from task (of 1 total lines):
[2024-12-10T17:58:55.788462Z] [fv-az525-427] [145627_1] [TaskManager] [ERROR] [2024-12-10T17:58:55.774532Z] [fv-az525-427] [145627_1] [getChromDepth_sample000_estimateChromDepth_000_chr21] /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/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
[2024-12-10T17:58:58.688849Z] [fv-az525-427] [145627_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2024-12-10T17:58:58.688895Z] [fv-az525-427] [145627_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/7bf95e035d07a296db4135640ce7bd60/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'
[2024-12-10T17:58:58.688924Z] [fv-az525-427] [145627_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Error Message:
[2024-12-10T17:58:58.688939Z] [fv-az525-427] [145627_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Last 1 stderr lines from task (of 1 total lines):
[2024-12-10T17:58:58.688939Z] [fv-az525-427] [145627_1] [WorkflowRunner] [ERROR] [2024-12-10T17:58:55.774532Z] [fv-az525-427] [145627_1] [getChromDepth_sample000_estimateChromDepth_000_chr21] /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/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
[2024-12-10T17:58:58.688959Z] [fv-az525-427] [145627_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/7bf95e035d07a296db4135640ce7bd60/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'
[2024-12-10T17:58:58.688977Z] [fv-az525-427] [145627_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2024-12-10T17:58:58.688995Z] [fv-az525-427] [145627_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Last 1 stderr lines from task (of 1 total lines):
[2024-12-10T17:58:58.688995Z] [fv-az525-427] [145627_1] [WorkflowRunner] [ERROR] [2024-12-10T17:58:55.689201Z] [fv-az525-427] [145627_1] [getAlignmentStats_generateStats_000] /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/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/7bf95e035d07a296db4135640ce7bd60/work/a5/9c22fcc7878091b3fc5346d90dd8b2
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '/home/runner/work/sarek/sarek/~/tests/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-
WARN: Killing running tasks (1)
Nextflow stderr:
Loading