Merge pull request #1752 from FriederikeHanssen/fullsize #6945
GitHub Actions / JUnit Test Report
failed
Dec 11, 2024 in 0s
9 tests run, 6 passed, 0 skipped, 3 failed.
Annotations
Check failure on line 1 in Test pipeline
github-actions / JUnit Test Report
Test pipeline.Run with profile test | --input tests/csv/3.0/fastq_pair.csv
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.11.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [high_pesquet] DSL2 - revision: 3954909713
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[0;32m,--.[0;30m/[0;32m,-.[0m
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[0;32m`._,._,'[0m
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[0;37m / [0;32m|\[0m`-_ \[0m [0;34m __ __ ___ [0m
[0;37m | [0;32m| \[0m `-|[0m [0;34m|__` /\ |__) |__ |__/[0m
[0;37m \ [0;32m| \[0m /[0m [0;34m.__| /¯¯\ | \ |___ | \[0m
[0;37m `[0;32m|[0m____[0;32m\[0m´[0m
[0;35m nf-core/sarek 3.5.0[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
[0;34minput : [0;32m/home/runner/work/sarek/sarek/tests/csv/3.0/fastq_pair.csv[0m
[0;34moutdir : [0;32m/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/output[0m
[1mMain options[0m
[0;34msplit_fastq : [0;32m0[0m
[0;34mintervals : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.interval_list[0m
[0;34mtools : [0;32mstrelka[0m
[1mAnnotation[0m
[0;34mbcftools_annotations : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz[0m
[0;34mbcftools_annotations_tbi : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi[0m
[0;34mbcftools_header_lines : [0;32m/home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt[0m
[1mGeneral reference genome options[0m
[0;34migenomes_base : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/[0m
[1mReference genome options[0m
[0;34mgenome : [0;32mtestdata.nf-core.sarek[0m
[0;34mdbsnp : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz[0m
[0;34mdbsnp_tbi : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi[0m
[0;34mdbsnp_vqsr : [0;32m--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz[0m
[0;34mdict : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict[0m
[0;34mfasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.fasta[0m
[0;34mfasta_fai : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.fasta.fai[0m
[0;34mgermline_resource : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz[0m
[0;34mgermline_resource_tbi : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi[0m
[0;34mknown_indels : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz[0m
[0;34mknown_indels_tbi : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi[0m
[0;34mknown_indels_vqsr : [0;32m--resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz[0m
[0;34mngscheckmate_bed : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed[0m
[0;34msentieon_dnascope_model : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model[0m
[0;34msnpeff_cache : [0;32mnull[0m
[0;34msnpeff_db : [0;32mWBcel235.105[0m
[0;34mvep_cache : [0;32mnull[0m
[0;34mvep_cache_version : [0;32m113[0m
[0;34mvep_genome : [0;32mWBcel235[0m
[0;34mvep_species : [0;32mcaenorhabditis_elegans[0m
[1mInstitutional config options[0m
[0;34mconfig_profile_name : [0;32mTest profile[0m
[0;34mconfig_profile_description: [0;32mMinimal test dataset to check pipeline function[0m
[0;34mmodules_testdata_base_path: [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/[0m
[1mCore Nextflow options[0m
[0;34mrunName : [0;32mhigh_pesquet[0m
[0;34mlaunchDir : [0;32m/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0[0m
[0;34mworkDir : [0;32m/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/sarek/sarek[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest,conda[0m
[0;34mconfigFiles : [0;32m[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* The pipeline
https://doi.org/10.12688/f1000research.16665.2
https://doi.org/10.1093/nargab/lqae031
https://doi.org/10.5281/zenodo.3476425
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/sarek/blob/master/CITATIONS.md
WARN: FASTQ file(/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz): Cannot extract flowcell ID from @normal#21#998579#1/1
WARN: FASTQ file(/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz): Cannot extract flowcell ID from @normal#21#998513#1/1
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-b45f4430b1ab9d6e-f9b4f646bf1b67e52890543d27cb2f27]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/gatk4/intervallisttobed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-73143911187759b2-d2d82a1cc7858810940ff84273e57b63]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/bwa/index/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-5f8479c2edf694ea-b7d45abbc59134ec734c2810969e7f00]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/fastqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-d3cbe95ac01651f4-3ea42529974ca5a54ae5623eacfbc76a]
[32/0c3256] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (genome.interval_list)
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-5a9ba0ebb7bcf86c-497b0f18c811c5671b5e17e0034188ed]
[39/8a48a6] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test2-test_L1)
[03/9a542f] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test-test_L1)
[5c/531005] 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]
[73/a05584] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED (genome)
[f0/5d3467] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test)
[b9/b638aa] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test2)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../../../modules/nf-core/gatk4/markduplicates/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-2421a9d4f9dcd0b1-7753f12b1b6af37c6e7eb5fd03e42240]
[aa/a7f1d7] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr22_1-40001)
[de/557ef9] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (genome)
[d6/136b8e] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (test)
[c6/0bec5a] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (test2)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-1abf3db016bf3fb9-873a3583ebab040412cb72c07ed757ab]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-c5b497d07713b814-57cd7e91fe23a8ceb488416c37dae89b]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_baserecalibrator/../../../modules/nf-core/gatk4/baserecalibrator/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-7d2dddae736a8a74-d2d82a1cc7858810940ff84273e57b63]
[59/2678a7] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test)
[7b/fd119d] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test2)
[93/63010a] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test2)
[3b/d94f52] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test)
[c7/9b6a0b] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (test)
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]
[af/fa0165] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (test2)
[49/fc2e80] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test2)
[22/b7bd9c] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_applybqsr/../cram_merge_index_samtools/../../../modules/nf-core/samtools/index/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-bc98654c03cc37f5-873a3583ebab040412cb72c07ed757ab]
[50/3327eb] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test2)
[40/6a389e] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test)
[79/a69caf] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (test2)
[d9/18016d] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_single_strelka/../../../modules/nf-core/strelka/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/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]
[91/e80553] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (test2)
[2f/c17d60] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (test)
[c3/4d47c1] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (test)
[ed/14a769] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_qc_bcftools_vcftools/../../../modules/nf-core/bcftools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-d14f40c429aefa2b-dc6f2c13cbbb0f956fd0966de87d7df8]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_qc_bcftools_vcftools/../../../modules/nf-core/vcftools/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-ac437bb99679f3c6-ede778c78582be405557f3c8ca0e9927]
[ed/14a769] 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)
[ab/fb9903] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (test2_vs_test)
[ab/fb9903] 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)
[93/31d095] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (test)
[3d/915883] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (test)
[72/e8c398] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (test)
[a2/fbb328] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (test)
[ec/47e8bc] 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:
[2024-12-11T09:38:24.939902Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] Launching command task: 'getChromDepth_sample000_catChromDepth' from master workflow
[2024-12-11T09:38:24.942282Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskRunner:getChromDepth_sample000_catChromDepth] Task initiated on local node
[2024-12-11T09:38:25.003668Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] Completed command task: 'getChromDepth_sample000_catChromDepth' launched from master workflow
[2024-12-11T09:38:25.003943Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] Launching command task: 'getChromDepth_mergeChromDepth' from master workflow
[2024-12-11T09:38:25.006281Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskRunner:getChromDepth_mergeChromDepth] Task initiated on local node
[2024-12-11T09:38:25.067760Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] Completed command task: 'getChromDepth_mergeChromDepth' launched from master workflow
[2024-12-11T09:38:25.068000Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2024-12-11T09:38:25.068145Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2024-12-11T09:38:25.068595Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2024-12-11T09:38:25.068750Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] Launching command task: 'getChromDepth_removeTmpDir' from master workflow
[2024-12-11T09:38:25.069273Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
[2024-12-11T09:38:25.069934Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
[2024-12-11T09:38:25.070316Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_000_chr22_0000' to sub-workflow 'CallGenome'
[2024-12-11T09:38:25.070962Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2024-12-11T09:38:25.071372Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2024-12-11T09:38:25.072796Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2024-12-11T09:38:25.073428Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskRunner:getChromDepth_removeTmpDir] Task initiated on local node
[2024-12-11T09:38:25.073896Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2024-12-11T09:38:25.074449Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2024-12-11T09:38:25.075355Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2024-12-11T09:38:25.077658Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2024-12-11T09:38:25.077812Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2024-12-11T09:38:25.078512Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2024-12-11T09:38:25.079049Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2024-12-11T09:38:25.110947Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2024-12-11T09:38:25.111021Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] Completed command task: 'getChromDepth_removeTmpDir' launched from master workflow
[2024-12-11T09:38:25.111300Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' from sub-workflow 'CallGenome'
[2024-12-11T09:38:25.113843Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_000_chr22_0000] Task initiated on local node
[2024-12-11T09:38:25.275404Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr22:1-40001 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr22_1-40001.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.recal.cram --tumor-align-file test2.recal.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr22_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr22_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr22_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-11T09:38:25.275490Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Error Message:
[2024-12-11T09:38:25.275508Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
[2024-12-11T09:38:25.275523Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Logging 5 line(s) of task wrapper log output below:
[2024-12-11T09:38:25.275539Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T09:38:25.128784Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] wrapperStart
[2024-12-11T09:38:25.275563Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T09:38:25.138973Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStart
[2024-12-11T09:38:25.275583Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T09:38:25.221450Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskExitCode -11
[2024-12-11T09:38:25.275597Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T09:38:25.222719Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStderrTail 1
[2024-12-11T09:38:25.275611Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-11T09:38:25.275629Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
[2024-12-11T09:38:26.090792Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2024-12-11T09:38:27.507852Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2024-12-11T09:38:27.507888Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr22_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr22:1-40001 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr22_1-40001.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/14ed1c6de97f743ae4153d1d9e2a1f0/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.recal.cram --tumor-align-file test2.recal.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr22_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr22_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr22_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-11T09:38:27.507921Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Error Message:
[2024-12-11T09:38:27.507934Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
[2024-12-11T09:38:27.507951Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] Logging 5 line(s) of task wrapper log output below:
[2024-12-11T09:38:27.507966Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T09:38:25.128784Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] wrapperStart
[2024-12-11T09:38:27.507981Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T09:38:25.138973Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStart
[2024-12-11T09:38:27.507996Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T09:38:25.221450Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskExitCode -11
[2024-12-11T09:38:27.508014Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] [2024-12-11T09:38:25.222719Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr22_0000] [wrapperSignal] taskStderrTail 1
[2024-12-11T09:38:27.508028Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr22_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-11T09:38:27.508045Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [125573_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/ec/47e8bc326335d3651601a8718809bc
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 24.11.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [nice_sax] DSL2 - revision: 3954909713
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;37m ____[0m
[0;37m .´ _ `.[0m
[0;37m / [0;32m|\[0m`-_ \[0m [0;34m __ __ ___ [0m
[0;37m | [0;32m| \[0m `-|[0m [0;34m|__` /\ |__) |__ |__/[0m
[0;37m \ [0;32m| \[0m /[0m [0;34m.__| /¯¯\ | \ |___ | \[0m
[0;37m `[0;32m|[0m____[0;32m\[0m´[0m
[0;35m nf-core/sarek 3.5.0[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
[0;34minput : [0;32m/home/runner/work/sarek/sarek/tests/csv/3.0/recalibrated.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;32mnice_sax[0m
[0;34mlaunchDir : [0;32m/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132[0m
[0;34mworkDir : [0;32m/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/sarek/sarek[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest,conda[0m
[0;34mconfigFiles : [0;32m[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* The pipeline
https://doi.org/10.12688/f1000research.16665.2
https://doi.org/10.1093/nargab/lqae031
https://doi.org/10.5281/zenodo.3476425
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/sarek/blob/master/CITATIONS.md
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-b45f4430b1ab9d6e-f9b4f646bf1b67e52890543d27cb2f27]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-5a9ba0ebb7bcf86c-497b0f18c811c5671b5e17e0034188ed]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-c5b497d07713b814-57cd7e91fe23a8ceb488416c37dae89b]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-1abf3db016bf3fb9-873a3583ebab040412cb72c07ed757ab]
[f4/f06a5f] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[fe/88876f] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[32/e17d50] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample2)
[f3/7aef85] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample1)
[84/2db72e] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[99/45dd91] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[7b/29c4c2] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[fb/c2b619] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample1)
[ef/861dea] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample2)
[98/f860df] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_2-23354000)
[7c/a53ae2] 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/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]
[84/401a80] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (sample1)
[01/cbe2a2] 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]
[47/dff6cc] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample1)
[01/cbe2a2] 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)
[92/dd6f13] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)
[92/dd6f13] 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)
[99/eae4aa] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample1)
[89/cd07c1] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample1)
[ce/16393c] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample1)
[b4/5b5ef5] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)'
Caused by:
Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1)
Command executed:
configureStrelkaSomaticWorkflow.py \
--tumor test2.paired_end.recalibrated.sorted.cram \
--normal test.paired_end.recalibrated.sorted.cram \
--referenceFasta genome.fasta \
--callRegions chr21_2-23354000.bed.gz \
\
\
--runDir strelka
sed -i s/"isEmail = isLocalSmtp()"/"isEmail = False"/g strelka/runWorkflow.py
python strelka/runWorkflow.py -m local -j 4
mv strelka/results/variants/somatic.indels.vcf.gz sample4_vs_sample3.strelka.somatic_indels.vcf.gz
mv strelka/results/variants/somatic.indels.vcf.gz.tbi sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
mv strelka/results/variants/somatic.snvs.vcf.gz sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
mv strelka/results/variants/somatic.snvs.vcf.gz.tbi sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC":
strelka: $( configureStrelkaSomaticWorkflow.py --version )
END_VERSIONS
Command exit status:
1
Command output:
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:
strelka/runWorkflow.py
Command error:
[2024-12-11T09:40:48.246377Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2024-12-11T09:40:48.224411Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStderrTail 1
[2024-12-11T09:40:48.246403Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-11T09:40:48.246506Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0003' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:35032489-46709983 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0003.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0003.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0003.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-11T09:40:48.246547Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Error Message:
[2024-12-11T09:40:48.246574Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/015/pyflowTaskWrapper.signal.txt'
[2024-12-11T09:40:48.246600Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Logging 5 line(s) of task wrapper log output below:
[2024-12-11T09:40:48.246625Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-11T09:40:48.022933Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] wrapperStart
[2024-12-11T09:40:48.246651Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-11T09:40:48.039712Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStart
[2024-12-11T09:40:48.246676Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-11T09:40:48.202725Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskExitCode -11
[2024-12-11T09:40:48.246709Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-11T09:40:48.203983Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStderrTail 1
[2024-12-11T09:40:48.246736Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-11T09:40:48.961730Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2024-12-11T09:40:51.580834Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2024-12-11T09:40:51.580892Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0001' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:11677497-23354992 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0001.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0001.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0001.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-11T09:40:51.580955Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Error Message:
[2024-12-11T09:40:51.580978Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/011/pyflowTaskWrapper.signal.txt'
[2024-12-11T09:40:51.581008Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] Logging 5 line(s) of task wrapper log output below:
[2024-12-11T09:40:51.581037Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-11T09:40:48.021703Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] wrapperStart
[2024-12-11T09:40:51.581063Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-11T09:40:48.031029Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStart
[2024-12-11T09:40:51.581091Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-11T09:40:48.170292Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskExitCode -11
[2024-12-11T09:40:51.581125Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] [2024-12-11T09:40:48.172231Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0001] [wrapperSignal] taskStderrTail 1
[2024-12-11T09:40:51.581152Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0001] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-11T09:40:51.581182Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2024-12-11T09:40:51.581207Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0002' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:23354993-35032488 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0002.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0002.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0002.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-11T09:40:51.581248Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Error Message:
[2024-12-11T09:40:51.581273Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/013/pyflowTaskWrapper.signal.txt'
[2024-12-11T09:40:51.581325Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] Logging 5 line(s) of task wrapper log output below:
[2024-12-11T09:40:51.581349Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2024-12-11T09:40:48.021134Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] wrapperStart
[2024-12-11T09:40:51.581377Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2024-12-11T09:40:48.032877Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskStart
[2024-12-11T09:40:51.581402Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2024-12-11T09:40:48.187738Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskExitCode -11
[2024-12-11T09:40:51.581425Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] [2024-12-11T09:40:48.189779Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0002] [wrapperSignal] taskStderrTail 1
[2024-12-11T09:40:51.581439Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0002] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-11T09:40:51.581454Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0003' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:35032489-46709983 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0003.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0003.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0003.xml --strelka-skip-header --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-11T09:40:51.581481Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Error Message:
[2024-12-11T09:40:51.581500Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/015/pyflowTaskWrapper.signal.txt'
[2024-12-11T09:40:51.581518Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] Logging 5 line(s) of task wrapper log output below:
[2024-12-11T09:40:51.581533Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-11T09:40:48.022933Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] wrapperStart
[2024-12-11T09:40:51.581549Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-11T09:40:48.039712Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStart
[2024-12-11T09:40:51.581564Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-11T09:40:48.202725Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskExitCode -11
[2024-12-11T09:40:51.581580Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] [2024-12-11T09:40:48.203983Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0003] [wrapperSignal] taskStderrTail 1
[2024-12-11T09:40:51.581601Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0003] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
[2024-12-11T09:40:51.581616Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr21_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/libexec/strelka2 --region chr21:1-11677496 --ref genome.fasta --max-indel-size 49 --call-regions-bed chr21_2-23354000.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/conda/env-45ec49f1ad56587b-438a505d7b44a08705c858f9ad6e02ce/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file test.paired_end.recalibrated.sorted.cram --tumor-align-file test2.paired_end.recalibrated.sorted.cram --somatic-snv-file strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr21_0000.vcf --somatic-indel-file strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr21_0000.vcf --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr21_0000.xml --strelka-chrom-depth-file strelka/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'
[2024-12-11T09:40:51.581641Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Error Message:
[2024-12-11T09:40:51.581654Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Anomalous task wrapper stderr output. Wrapper signal file: 'strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/008/pyflowTaskWrapper.signal.txt'
[2024-12-11T09:40:51.581670Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] Logging 5 line(s) of task wrapper log output below:
[2024-12-11T09:40:51.581689Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2024-12-11T09:40:48.044963Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] wrapperStart
[2024-12-11T09:40:51.581705Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2024-12-11T09:40:48.064281Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStart
[2024-12-11T09:40:51.581721Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2024-12-11T09:40:48.221942Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskExitCode -11
[2024-12-11T09:40:51.581737Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] [2024-12-11T09:40:48.224411Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_000_chr21_0000] [wrapperSignal] taskStderrTail 1
[2024-12-11T09:40:51.581752Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [131794_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr21_0000] [taskWrapper-stderr] Last 0 stderr lines from task (of 0 total lines):
Work dir:
/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/work/b4/5b5ef5cb3761b124dc7cd86209c214
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- Check '/home/runner/work/sarek/sarek/~/tests/fa9ac3ed693ca54cacee2f6c2755132/meta/nextflow.log' file for details
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 24.11.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [lonely_wiles] DSL2 - revision: 3954909713
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
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[0;32m`._,._,'[0m
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[0;37m | [0;32m| \[0m `-|[0m [0;34m|__` /\ |__) |__ |__/[0m
[0;37m \ [0;32m| \[0m /[0m [0;34m.__| /¯¯\ | \ |___ | \[0m
[0;37m `[0;32m|[0m____[0;32m\[0m´[0m
[0;35m nf-core/sarek 3.5.0[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
[0;34minput : [0;32m/home/runner/work/sarek/sarek/tests/csv/3.0/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;32mlonely_wiles[0m
[0;34mlaunchDir : [0;32m/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60[0m
[0;34mworkDir : [0;32m/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/sarek/sarek[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest,conda[0m
[0;34mconfigFiles : [0;32m[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* The pipeline
https://doi.org/10.12688/f1000research.16665.2
https://doi.org/10.1093/nargab/lqae031
https://doi.org/10.5281/zenodo.3476425
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/sarek/blob/master/CITATIONS.md
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/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/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-b45f4430b1ab9d6e-f9b4f646bf1b67e52890543d27cb2f27]
Creating env using conda: /home/runner/work/sarek/sarek/./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]
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]
[c6/bea678] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_germline_manta/../../../modules/nf-core/manta/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-30739cc20e367bec-86f8fc4b934d0b08515f88ef4592bd1f]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_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]
[04/9d9d05] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample3)
[f6/20677f] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample4)
[02/19bcea] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample4)
[3a/95e035] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample3)
[6b/890082] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
[91/9664a5] 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/7bf95e035d07a296db4135640ce7bd60/work/conda/env-90ad7ffecab6b5bf-438a505d7b44a08705c858f9ad6e02ce]
[3c/a63afc] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
[94/31f39d] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
[3c/a63afc] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1) -- Execution is retried (1)
[94/31f39d] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)` terminated with an error exit status (1) -- Execution is retried (1)
[82/ef5777] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (sample3)
[4f/e74774] Re-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]
[4f/e74774] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1) -- Execution is retried (2)
[ab/bf88af] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
[ab/bf88af] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)` terminated with an error exit status (1) -- Execution is retried (2)
[bd/5a000c] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (sample3)
[31/730073] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (sample3)
[c3/8cefe1] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (sample3)
[bb/7b6bb6] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (sample3)
[19/722792] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)
[04/26c5a6] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (sample3)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)'
Caused by:
Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (sample4_vs_sample3)` terminated with an error exit status (1)
Command executed:
configManta.py \
--tumorBam test2.paired_end.recalibrated.sorted.cram \
--normalBam test.paired_end.recalibrated.sorted.cram \
--reference genome.fasta \
\
--runDir manta \
--callRegions multi_intervals.bed.gz \
python manta/runWorkflow.py -m local -j 4
mv manta/results/variants/candidateSmallIndels.vcf.gz \
sample4_vs_sample3.manta.candidate_small_indels.vcf.gz
mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \
sample4_vs_sample3.manta.candidate_small_indels.vcf.gz.tbi
mv manta/results/variants/candidateSV.vcf.gz \
sample4_vs_sample3.manta.candidate_sv.vcf.gz
mv manta/results/variants/candidateSV.vcf.gz.tbi \
sample4_vs_sample3.manta.candidate_sv.vcf.gz.tbi
mv manta/results/variants/diploidSV.vcf.gz \
sample4_vs_sample3.manta.diploid_sv.vcf.gz
mv manta/results/variants/diploidSV.vcf.gz.tbi \
sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
mv manta/results/variants/somaticSV.vcf.gz \
sample4_vs_sample3.manta.somatic_sv.vcf.gz
mv manta/results/variants/somaticSV.vcf.gz.tbi \
sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC":
manta: $( configManta.py --version )
END_VERSIONS
Command exit status:
1
Command output:
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:
manta/runWorkflow.py
Command error:
[2024-12-11T09:54:57.695264Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_001] Task initiated on local node
[2024-12-11T09:54:57.696541Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2024-12-11T09:54:57.723010Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getChromDepth_sample000_makeTmpDir] Task initiated on local node
[2024-12-11T09:54:57.723346Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_001] [WARNING] Task: 'getAlignmentStats_generateStats_001' failed but qualifies for retry. Total task failures (including this one): 1. Task command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.001.xml --align-file test2.paired_end.recalibrated.sorted.cram'
[2024-12-11T09:54:57.733108Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_000] [WARNING] Task: 'getAlignmentStats_generateStats_000' failed but qualifies for retry. Total task failures (including this one): 1. Task command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
[2024-12-11T09:54:57.755448Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] Completed command task: 'getChromDepth_sample000_makeTmpDir' launched from master workflow
[2024-12-11T09:54:57.756182Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] Launching command task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' from master workflow
[2024-12-11T09:54:57.758666Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
[2024-12-11T09:54:57.786008Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] [WARNING] Task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' failed but qualifies for retry. Total task failures (including this one): 1. Task command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth --ref genome.fasta --align-file test.paired_end.recalibrated.sorted.cram --output manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chr21 --chrom chr21'
[2024-12-11T09:56:27.813528Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_001] Retrying task: 'getAlignmentStats_generateStats_001'. Total prior task failures: 1
[2024-12-11T09:56:27.816217Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_001] Task initiated on local node
[2024-12-11T09:56:27.822517Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_000] Retrying task: 'getAlignmentStats_generateStats_000'. Total prior task failures: 1
[2024-12-11T09:56:27.824615Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2024-12-11T09:56:27.847412Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_001] [WARNING] Task: 'getAlignmentStats_generateStats_001' failed but qualifies for retry. Total task failures (including this one): 2. Task command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.001.xml --align-file test2.paired_end.recalibrated.sorted.cram'
[2024-12-11T09:56:27.854543Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_000] [WARNING] Task: 'getAlignmentStats_generateStats_000' failed but qualifies for retry. Total task failures (including this one): 2. Task command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
[2024-12-11T09:56:27.873377Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Retrying task: 'getChromDepth_sample000_estimateChromDepth_000_chr21'. Total prior task failures: 1
[2024-12-11T09:56:27.875321Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
[2024-12-11T09:56:27.904489Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] [WARNING] Task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' failed but qualifies for retry. Total task failures (including this one): 2. Task command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth --ref genome.fasta --align-file test.paired_end.recalibrated.sorted.cram --output manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chr21 --chrom chr21'
[2024-12-11T09:57:57.900767Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_001] Retrying task: 'getAlignmentStats_generateStats_001'. Total prior task failures: 2
[2024-12-11T09:57:57.903411Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_001] Task initiated on local node
[2024-12-11T09:57:57.941378Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_000] Retrying task: 'getAlignmentStats_generateStats_000'. Total prior task failures: 2
[2024-12-11T09:57:57.943466Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2024-12-11T09:57:57.947431Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_001' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.001.xml --align-file test2.paired_end.recalibrated.sorted.cram'
[2024-12-11T09:57:57.947670Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_001] Error Message:
[2024-12-11T09:57:57.947786Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_001] Last 1 stderr lines from task (of 1 total lines):
[2024-12-11T09:57:57.947786Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] [2024-12-11T09:57:57.925598Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [getAlignmentStats_generateStats_001] /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
[2024-12-11T09:57:57.948044Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
[2024-12-11T09:57:57.980193Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
[2024-12-11T09:57:57.980243Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2024-12-11T09:57:57.980269Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 1 stderr lines from task (of 1 total lines):
[2024-12-11T09:57:57.980269Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] [2024-12-11T09:57:57.965560Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [getAlignmentStats_generateStats_000] /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
[2024-12-11T09:57:57.993346Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Retrying task: 'getChromDepth_sample000_estimateChromDepth_000_chr21'. Total prior task failures: 2
[2024-12-11T09:57:57.995485Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_chr21] Task initiated on local node
[2024-12-11T09:57:58.044367Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth --ref genome.fasta --align-file test.paired_end.recalibrated.sorted.cram --output manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chr21 --chrom chr21'
[2024-12-11T09:57:58.044439Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Error Message:
[2024-12-11T09:57:58.044471Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Last 1 stderr lines from task (of 1 total lines):
[2024-12-11T09:57:58.044471Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [TaskManager] [ERROR] [2024-12-11T09:57:58.017367Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [getChromDepth_sample000_estimateChromDepth_000_chr21] /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
[2024-12-11T09:58:00.904490Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2024-12-11T09:58:00.904533Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file test.paired_end.recalibrated.sorted.cram'
[2024-12-11T09:58:00.904560Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2024-12-11T09:58:00.904576Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Last 1 stderr lines from task (of 1 total lines):
[2024-12-11T09:58:00.904576Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] [2024-12-11T09:57:57.965560Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [getAlignmentStats_generateStats_000] /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
[2024-12-11T09:58:00.904598Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_001' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats --ref genome.fasta --output-file manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.001.xml --align-file test2.paired_end.recalibrated.sorted.cram'
[2024-12-11T09:58:00.904620Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_001] Error Message:
[2024-12-11T09:58:00.904633Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_001] Last 1 stderr lines from task (of 1 total lines):
[2024-12-11T09:58:00.904633Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] [2024-12-11T09:57:57.925598Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [getAlignmentStats_generateStats_001] /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetAlignmentStats: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
[2024-12-11T09:58:00.904656Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_000_chr21' launched from master workflow, error code: 127, command: '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth --ref genome.fasta --align-file test.paired_end.recalibrated.sorted.cram --output manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.000.txt_000_chr21 --chrom chr21'
[2024-12-11T09:58:00.904681Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Error Message:
[2024-12-11T09:58:00.904696Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] [getChromDepth_sample000_estimateChromDepth_000_chr21] Last 1 stderr lines from task (of 1 total lines):
[2024-12-11T09:58:00.904696Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [WorkflowRunner] [ERROR] [2024-12-11T09:57:58.017367Z] [fv-az1152-306.ykhc0jfl13aufdxrnlto1juhnc.cx.internal.cloudapp.net] [146893_1] [getChromDepth_sample000_estimateChromDepth_000_chr21] /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-54e5ca2283cd7562-86f8fc4b934d0b08515f88ef4592bd1f/libexec/GetChromDepth: error while loading shared libraries: libboost_filesystem.so.1.85.0: cannot open shared object file: No such file or directory
Work dir:
/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/19/722792229eb027c8ea6e82232db504
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '/home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/meta/nextflow.log' file for details
Join mismatch for the following entries: key=[id:sample4_vs_sample3, normal_id:sample3, patient:test3, sex:XX, tumor_id:sample4] values=
-[0;35m[nf-core/sarek][0;31m Pipeline completed with errors[0m-
WARN: Killing running tasks (1)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/multiqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7bf95e035d07a296db4135640ce7bd60/work/conda/env-7da4088df3b01749-eec4e05336245ea50db6412788f8c4da]
Nextflow stderr:
Loading