Update .github/workflows/cloudtest.yml #6737
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failed
Feb 17, 2025 in 0s
9 tests run, 6 passed, 0 skipped, 3 failed.
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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 25.01.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [berserk_tesla] DSL2 - revision: 3954909713
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[0;37m \ [0;32m| \[0m /[0m [0;34m.__| /¯¯\ | \ |___ | \[0m
[0;37m `[0;32m|[0m____[0;32m\[0m´[0m
[0;35m nf-core/sarek 3.5.1[0m
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[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;32mberserk_tesla[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/home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/conf/test.config[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/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/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-b45f4430b1ab9d6e-47b5d3c40746bfdb673888286797637b]
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]
[28/faaa7a] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED (genome)
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]
[71/b6661f] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test2-test_L1)
[22/476ad9] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test-test_L1)
[2b/71fbc1] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (genome.interval_list)
[00/ebe532] 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]
[5a/831f13] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr22_1-40001)
[b6/7d6770] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (genome)
[02/7b7731] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test2)
[74/76ace7] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test)
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]
[8d/b29dcb] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (test2)
[78/969514] 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/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]
[75/a27538] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test2)
[03/050edc] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test)
[fa/2a6e50] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test)
[8a/db035f] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test2)
[90/2a4ca6] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (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]
[1c/c8fcd2] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (test)
[1a/b9bb53] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test)
[95/333af1] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test2)
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]
[e4/8534bb] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test2)
[8a/37f0f1] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test)
[05/995335] 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_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]
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]
[70/fe88eb] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (test)
[f1/6d9c26] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (test2)
[7e/ea92a6] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (test)
[32/86f957] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (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]
[60/c3ef61] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)
[6f/3e02d2] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (test)
[70/4c4a66] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (test)
[60/c3ef61] 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)
[5a/723353] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (test)
[b0/9344bc] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)
[b0/9344bc] 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)
[43/246705] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (test)
[1f/7f6b36] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)
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:
[2025-02-17T18:15:14.789985Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] Launching command task: 'getChromDepth_sample000_catChromDepth' from master workflow
[2025-02-17T18:15:14.792416Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskRunner:getChromDepth_sample000_catChromDepth] Task initiated on local node
[2025-02-17T18:15:14.853824Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] Completed command task: 'getChromDepth_sample000_catChromDepth' launched from master workflow
[2025-02-17T18:15:14.854165Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] Launching command task: 'getChromDepth_mergeChromDepth' from master workflow
[2025-02-17T18:15:14.856585Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskRunner:getChromDepth_mergeChromDepth] Task initiated on local node
[2025-02-17T18:15:14.917963Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] Completed command task: 'getChromDepth_mergeChromDepth' launched from master workflow
[2025-02-17T18:15:14.918204Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2025-02-17T18:15:14.918344Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2025-02-17T18:15:14.918881Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2025-02-17T18:15:14.919238Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] Launching command task: 'getChromDepth_removeTmpDir' from master workflow
[2025-02-17T18:15:14.919497Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
[2025-02-17T18:15:14.920034Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
[2025-02-17T18:15:14.920801Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2025-02-17T18:15:14.921068Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
[2025-02-17T18:15:14.923195Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskRunner:getChromDepth_removeTmpDir] Task initiated on local node
[2025-02-17T18:15:14.923488Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2025-02-17T18:15:14.924306Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2025-02-17T18:15:14.924634Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2025-02-17T18:15:14.924948Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2025-02-17T18:15:14.925327Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2025-02-17T18:15:14.927507Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2025-02-17T18:15:14.927987Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2025-02-17T18:15:14.928462Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2025-02-17T18:15:14.928840Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2025-02-17T18:15:14.961446Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] Completed command task: 'getChromDepth_removeTmpDir' launched from master workflow
[2025-02-17T18:15:14.961506Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2025-02-17T18:15:14.961770Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' from sub-workflow 'CallGenome'
[2025-02-17T18:15:14.963977Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_000_chr22_0000] Task initiated on local node
[2025-02-17T18:15:15.125712Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_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'
[2025-02-17T18:15:15.125790Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Error Message:
[2025-02-17T18:15:15.125811Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_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'
[2025-02-17T18:15:15.125831Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:15:15.125859Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2025-02-17T18:15:14.977982Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] wrapperStart
[2025-02-17T18:15:15.125891Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2025-02-17T18:15:14.983164Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStart
[2025-02-17T18:15:15.125921Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2025-02-17T18:15:15.081662Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskExitCode -11
[2025-02-17T18:15:15.125941Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2025-02-17T18:15:15.083695Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:15:15.125965Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:15:15.125984Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
[2025-02-17T18:15:15.941126Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2025-02-17T18:15:17.358307Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2025-02-17T18:15:17.358341Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_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'
[2025-02-17T18:15:17.358386Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Error Message:
[2025-02-17T18:15:17.358400Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_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'
[2025-02-17T18:15:17.358411Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:15:17.358427Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2025-02-17T18:15:14.977982Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] wrapperStart
[2025-02-17T18:15:17.358439Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2025-02-17T18:15:14.983164Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStart
[2025-02-17T18:15:17.358454Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2025-02-17T18:15:15.081662Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskExitCode -11
[2025-02-17T18:15:17.358466Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2025-02-17T18:15:15.083695Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:15:17.358479Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:15:17.358491Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [132979_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/1f/7f6b369e7ef3d11cd331efdf9baa11
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/meta/nextflow.log' file for details
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]
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-
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 25.01.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [prickly_goodall] 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 3.5.1[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;32mprickly_goodall[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/home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/conf/test.config[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/env-5a9ba0ebb7bcf86c-497b0f18c811c5671b5e17e0034188ed]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-b45f4430b1ab9d6e-47b5d3c40746bfdb673888286797637b]
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]
[30/7deefb] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)
[a0/1cd936] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[25/594302] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[36/ae7792] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample2)
[6b/6a1be5] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample1)
[7e/3f351f] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample2)
[ee/c84fa3] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[02/f929bc] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[ca/5f9976] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample1)
[fd/7edf55] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[c3/615de2] 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_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]
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]
[27/6dfab3] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (sample1)
[ef/5e80eb] 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]
[4e/c50641] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample1)
[ef/5e80eb] 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)
[3b/d7d1eb] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)
[3b/d7d1eb] 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)
[2d/f076fa] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample1)
[07/8a99ef] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample1)
[16/99e176] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample1)
[cd/ef9b13] 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:
[2025-02-17T18:17:36.217949Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:17:36.199427Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:17:36.217971Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:17:36.229925Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [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'
[2025-02-17T18:17:36.230442Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Error Message:
[2025-02-17T18:17:36.230500Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [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'
[2025-02-17T18:17:36.230921Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:17:36.230956Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:17:35.960750Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] wrapperStart
[2025-02-17T18:17:36.230986Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:17:35.968895Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStart
[2025-02-17T18:17:36.231023Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:17:36.210551Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskExitCode -11
[2025-02-17T18:17:36.231063Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:17:36.215565Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:17:36.231094Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:17:36.950046Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2025-02-17T18:17:39.569116Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2025-02-17T18:17:39.569176Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_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'
[2025-02-17T18:17:39.569210Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Error Message:
[2025-02-17T18:17:39.569220Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_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'
[2025-02-17T18:17:39.569236Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:17:39.569248Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:17:35.960750Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] wrapperStart
[2025-02-17T18:17:39.569260Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:17:35.968895Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStart
[2025-02-17T18:17:39.569273Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:17:36.210551Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskExitCode -11
[2025-02-17T18:17:39.569291Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:17:36.215565Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:17:39.569303Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:17:39.569320Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_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'
[2025-02-17T18:17:39.569342Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Error Message:
[2025-02-17T18:17:39.569352Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_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'
[2025-02-17T18:17:39.569392Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:17:39.569416Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:17:35.964976Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] wrapperStart
[2025-02-17T18:17:39.569430Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:17:35.972977Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStart
[2025-02-17T18:17:39.569441Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:17:36.197053Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskExitCode -11
[2025-02-17T18:17:39.569451Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:17:36.199247Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:17:39.569466Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:17:39.569476Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2025-02-17T18:17:39.569486Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_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'
[2025-02-17T18:17:39.569509Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Error Message:
[2025-02-17T18:17:39.569518Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_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'
[2025-02-17T18:17:39.569532Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:17:39.569542Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:17:35.959200Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] wrapperStart
[2025-02-17T18:17:39.569554Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:17:35.967383Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskStart
[2025-02-17T18:17:39.569565Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:17:36.160608Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskExitCode -11
[2025-02-17T18:17:39.569577Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:17:36.165672Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:17:39.569591Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:17:39.569601Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_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'
[2025-02-17T18:17:39.569623Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Error Message:
[2025-02-17T18:17:39.569632Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_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'
[2025-02-17T18:17:39.569642Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:17:39.569657Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:17:35.962797Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] wrapperStart
[2025-02-17T18:17:39.569668Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:17:35.972268Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStart
[2025-02-17T18:17:39.569680Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:17:36.196802Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskExitCode -11
[2025-02-17T18:17:39.569690Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:17:36.199427Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:17:39.569703Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [139605_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
Work dir:
/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/cd/ef9b13d67682c926a9430bce3e9290
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
-- Check '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/meta/nextflow.log' file for details
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]
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:
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 25.01.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [friendly_wozniak] 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 3.5.1[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;32mfriendly_wozniak[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/home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/conf/test.config[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-47b5d3c40746bfdb673888286797637b]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/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]
[43/538666] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[b5/df6d3e] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[d4/580794] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[c6/fb059e] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[17/5552b5] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[8d/67368b] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_2-23354000)
[b0/f69414] 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/env-90ad7ffecab6b5bf-438a505d7b44a08705c858f9ad6e02ce]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_germline_manta/../../../modules/nf-core/manta/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f]
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]
[68/c88611] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (sample3)
[ea/08f54a] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_qc_bcftools_vcftools/../../../modules/nf-core/bcftools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/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]
[e4/75665a] 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/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_strelka/../../../modules/nf-core/strelka/somatic/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce]
[13/5b10e9] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample3)
[e1/919917] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample3)
[54/5961a8] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample3)
[5d/092310] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample3)
[96/5bc42e] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample4_vs_sample3)
[ac/e0679f] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample4_vs_sample3)
[15/035bdc] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample4_vs_sample3)
[24/33dd14] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample4_vs_sample3)
[8a/1701fd] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample4_vs_sample3)
[6a/768ada] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample4_vs_sample3)
[f8/22d99e] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample4_vs_sample3)
[dd/ff89a1] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample4_vs_sample3)
[3f/626ab5] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample3)
[06/0a903e] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample3)
[ae/6b121a] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample3)
[65/e0a5d3] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample3)
[2d/360de4] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)
[2d/360de4] 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)
[94/a30be8] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)
[94/a30be8] 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)
[44/80bc16] 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 \
--indelCandidates sample4_vs_sample3.manta.candidate_small_indels.vcf.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:
[2025-02-17T18:20:09.989109Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:20:09.977723Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:20:09.989136Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:20:09.989248Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [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/7bf95e035d07a296db4135640ce7bd60/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:1-11677496 --ref genome.fasta --max-indel-size 49 --candidate-indel-input-vcf sample4_vs_sample3.manta.candidate_small_indels.vcf.gz --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/7bf95e035d07a296db4135640ce7bd60/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/7bf95e035d07a296db4135640ce7bd60/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'
[2025-02-17T18:20:09.989310Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Error Message:
[2025-02-17T18:20:09.989342Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [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'
[2025-02-17T18:20:09.989409Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:20:09.989452Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:20:09.745257Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] wrapperStart
[2025-02-17T18:20:09.989492Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:20:09.753069Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStart
[2025-02-17T18:20:09.989521Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:20:09.957129Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskExitCode -11
[2025-02-17T18:20:09.989547Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:20:09.959692Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:20:09.989579Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:20:10.706743Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2025-02-17T18:20:13.326487Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2025-02-17T18:20:13.326537Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_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/7bf95e035d07a296db4135640ce7bd60/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:1-11677496 --ref genome.fasta --max-indel-size 49 --candidate-indel-input-vcf sample4_vs_sample3.manta.candidate_small_indels.vcf.gz --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/7bf95e035d07a296db4135640ce7bd60/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/7bf95e035d07a296db4135640ce7bd60/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'
[2025-02-17T18:20:13.326571Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Error Message:
[2025-02-17T18:20:13.326582Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_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'
[2025-02-17T18:20:13.326600Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:20:13.326614Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:20:09.745257Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] wrapperStart
[2025-02-17T18:20:13.326631Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:20:09.753069Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStart
[2025-02-17T18:20:13.326646Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:20:09.957129Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskExitCode -11
[2025-02-17T18:20:13.326660Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2025-02-17T18:20:09.959692Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:20:13.326673Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:20:13.326688Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_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/7bf95e035d07a296db4135640ce7bd60/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:35032489-46709983 --ref genome.fasta --max-indel-size 49 --candidate-indel-input-vcf sample4_vs_sample3.manta.candidate_small_indels.vcf.gz --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/7bf95e035d07a296db4135640ce7bd60/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/7bf95e035d07a296db4135640ce7bd60/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'
[2025-02-17T18:20:13.326714Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Error Message:
[2025-02-17T18:20:13.326723Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_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'
[2025-02-17T18:20:13.326738Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:20:13.326749Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:20:09.748179Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] wrapperStart
[2025-02-17T18:20:13.326765Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:20:09.756699Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStart
[2025-02-17T18:20:13.326775Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:20:09.974326Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskExitCode -11
[2025-02-17T18:20:13.326788Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2025-02-17T18:20:09.975800Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:20:13.326800Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:20:13.326811Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2025-02-17T18:20:13.326823Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_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/7bf95e035d07a296db4135640ce7bd60/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:11677497-23354992 --ref genome.fasta --max-indel-size 49 --candidate-indel-input-vcf sample4_vs_sample3.manta.candidate_small_indels.vcf.gz --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/7bf95e035d07a296db4135640ce7bd60/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/7bf95e035d07a296db4135640ce7bd60/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'
[2025-02-17T18:20:13.326847Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Error Message:
[2025-02-17T18:20:13.326857Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_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'
[2025-02-17T18:20:13.326869Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:20:13.326881Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:20:09.746194Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] wrapperStart
[2025-02-17T18:20:13.326896Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:20:09.756514Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStart
[2025-02-17T18:20:13.326909Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:20:09.975638Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskExitCode -11
[2025-02-17T18:20:13.326921Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2025-02-17T18:20:09.977723Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:20:13.326934Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2025-02-17T18:20:13.326945Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_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/7bf95e035d07a296db4135640ce7bd60/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:23354993-35032488 --ref genome.fasta --max-indel-size 49 --candidate-indel-input-vcf sample4_vs_sample3.manta.candidate_small_indels.vcf.gz --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/7bf95e035d07a296db4135640ce7bd60/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/7bf95e035d07a296db4135640ce7bd60/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'
[2025-02-17T18:20:13.326969Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Error Message:
[2025-02-17T18:20:13.326978Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_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'
[2025-02-17T18:20:13.326991Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Logging 5 line(s) of task wrapper log output below:
[2025-02-17T18:20:13.327002Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:20:09.743847Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] wrapperStart
[2025-02-17T18:20:13.327018Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:20:09.753351Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskStart
[2025-02-17T18:20:13.327028Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:20:09.959949Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskExitCode -11
[2025-02-17T18:20:13.327040Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2025-02-17T18:20:09.961457Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskStderrTail 1
[2025-02-17T18:20:13.327053Z] [fv-az1970-919.jylfb2lvhi2edjyxod04kr2g0d.cx.internal.cloudapp.net] [149875_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/7bf95e035d07a296db4135640ce7bd60/work/44/80bc160af25c7c82307e633167c072
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/meta/nextflow.log' file for details
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/env-7da4088df3b01749-eec4e05336245ea50db6412788f8c4da]
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-
Nextflow stderr:
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