Merge pull request #1748 from FriederikeHanssen/release_350 #6936
GitHub Actions / JUnit Test Report
failed
Dec 10, 2024 in 0s
8 tests run, 5 passed, 0 skipped, 3 failed.
Annotations
Check failure on line 1 in Test sentieon
github-actions / JUnit Test Report
Test sentieon.stub
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.04.2
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [admiring_northcutt] DSL2 - revision: 3954909713
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;37m ____[0m
[0;37m .´ _ `.[0m
[0;37m / [0;32m|\[0m`-_ \[0m [0;34m __ __ ___ [0m
[0;37m | [0;32m| \[0m `-|[0m [0;34m|__` /\ |__) |__ |__/[0m
[0;37m \ [0;32m| \[0m /[0m [0;34m.__| /¯¯\ | \ |___ | \[0m
[0;37m `[0;32m|[0m____[0;32m\[0m´[0m
[0;35m nf-core/sarek 3.5.0[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
[0;34minput : [0;32m/home/runner/work/sarek/sarek/tests/csv/3.0/fastq_single.csv[0m
[0;34moutdir : [0;32m/home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/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
[1mPreprocessing[0m
[0;34maligner : [0;32msentieon-bwamem[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;32madmiring_northcutt[0m
[0;34mlaunchDir : [0;32m/home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18[0m
[0;34mworkDir : [0;32m/home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/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: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected.
HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.
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/test_1.fastq.gz): Cannot extract flowcell ID from @normal#21#998579#1/1
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/bwa/index/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/work/conda/environment-b7d45abbc59134ec734c2810969e7f00]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/work/conda/gawk-f9b4f646bf1b67e52890543d27cb2f27]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/gatk4/intervallisttobed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/work/conda/environment-d2d82a1cc7858810940ff84273e57b63]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/fastqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/work/conda/environment-3ea42529974ca5a54ae5623eacfbc76a]
[7e/56c85d] 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/sentieon/bwamem/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/work/conda/environment-8588de915f3da4d31da1c88ef9fcafb3]
[df/8ddfa4] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test-test_L1)
[3d/b59601] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test-test_L2)
[07/4b00c3] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED (genome)
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/work/conda/environment-497b0f18c811c5671b5e17e0034188ed]
[f3/1679de] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (genome.interval_list)
[16/37649b] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (genome.stub)
[4a/192a50] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (genome)
[fc/b000b3] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:SENTIEON_BWAMEM (test-test_L2)
[63/0fbf44] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:SENTIEON_BWAMEM (test-test_L1)
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/19a0e9021a4e9f444d6500b601213d18/work/conda/environment-7753f12b1b6af37c6e7eb5fd03e42240]
[38/e7cded] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/work/conda/environment-873a3583ebab040412cb72c07ed757ab]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/work/conda/environment-57cd7e91fe23a8ceb488416c37dae89b]
[f1/a19946] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test)
[5c/e3b75c] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test)
[10/65778e] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test)
[c8/cbcaae] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test)
[30/b23489] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (test)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (1)'
Caused by:
java.nio.channels.OverlappingFileLockException
-- Check '/home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/meta/nextflow.log' file for details
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/19a0e9021a4e9f444d6500b601213d18/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce]
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/runner/work/sarek/sarek/~/tests/19a0e9021a4e9f444d6500b601213d18/meta/nextflow.log' file for details
-[0;35m[nf-core/sarek][0;31m Pipeline completed with errors[0m-
WARN: Killing running tasks (1)
Nextflow stderr:
Nextflow 24.10.2 is available - Please consider updating your version to it
Check failure on line 1 in Test pipeline when starting from prepare recalibration
github-actions / JUnit Test Report
Test pipeline when starting from prepare recalibration.Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --tools null
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.04.2
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [naughty_hamilton] 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/mapped_single_bam.csv[0m
[0;34mstep : [0;32mprepare_recalibration[0m
[0;34moutdir : [0;32m/home/runner/work/sarek/sarek/~/tests/8775f65882b5c2d60afd882794090111/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
[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;32mnaughty_hamilton[0m
[0;34mlaunchDir : [0;32m/home/runner/work/sarek/sarek/~/tests/8775f65882b5c2d60afd882794090111[0m
[0;34mworkDir : [0;32m/home/runner/work/sarek/sarek/~/tests/8775f65882b5c2d60afd882794090111/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/8775f65882b5c2d60afd882794090111/work/conda/gawk-f9b4f646bf1b67e52890543d27cb2f27]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/gatk4/intervallisttobed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/8775f65882b5c2d60afd882794090111/work/conda/environment-d2d82a1cc7858810940ff84273e57b63]
[9b/0e8701] 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/8775f65882b5c2d60afd882794090111/work/conda/environment-497b0f18c811c5671b5e17e0034188ed]
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (1)'
Caused by:
java.nio.channels.OverlappingFileLockException
-- Check '/home/runner/work/sarek/sarek/~/tests/8775f65882b5c2d60afd882794090111/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/runner/work/sarek/sarek/~/tests/8775f65882b5c2d60afd882794090111/meta/nextflow.log' file for details
-[0;35m[nf-core/sarek][0;31m Pipeline completed with errors[0m-
Join mismatch for the following entries: key=[patient:test, sample:test, sex:NA, status:0, id:test, data_type:bam] values=
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/multiqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/8775f65882b5c2d60afd882794090111/work/conda/environment-eec4e05336245ea50db6412788f8c4da]
Nextflow stderr:
Nextflow 24.10.2 is available - Please consider updating your version to it
Check failure on line 1 in Test pipeline
github-actions / JUnit Test Report
Test pipeline.Run with profile test | --tools controlfreec --no_intervals | tumoronly
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.04.2
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [furious_blackwell] 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_tumoronly.csv[0m
[0;34mstep : [0;32mvariant_calling[0m
[0;34moutdir : [0;32m/home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/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;34mno_intervals : [0;32mtrue[0m
[0;34mwes : [0;32mtrue[0m
[0;34mtools : [0;32mcontrolfreec[0m
[1mAnnotation[0m
[0;34mbcftools_annotations : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz[0m
[0;34mbcftools_annotations_tbi : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi[0m
[0;34mbcftools_header_lines : [0;32m/home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt[0m
[1mGeneral reference genome options[0m
[0;34migenomes_base : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/[0m
[1mReference genome options[0m
[0;34mgenome : [0;32mtestdata.nf-core.sarek[0m
[0;34mchr_dir : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz[0m
[0;34mdbsnp : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz[0m
[0;34mdbsnp_tbi : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi[0m
[0;34mdbsnp_vqsr : [0;32m--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz[0m
[0;34mdict : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict[0m
[0;34mfasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta[0m
[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;32mfurious_blackwell[0m
[0;34mlaunchDir : [0;32m/home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1[0m
[0;34mworkDir : [0;32m/home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/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/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/environment-497b0f18c811c5671b5e17e0034188ed]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/untar/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/environment-cac18ad63488da9f5109ab1f794a29f6]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/environment-57cd7e91fe23a8ceb488416c37dae89b]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_tumor_only_all/../bam_variant_calling_mpileup/../../../modules/nf-core/samtools/mpileup/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/environment-873a3583ebab040412cb72c07ed757ab]
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (1)'
Caused by:
java.nio.channels.OverlappingFileLockException
-- Check '/home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/meta/nextflow.log' file for details
-[0;35m[nf-core/sarek][0;31m Pipeline completed with errors[0m-
Nextflow stderr:
Nextflow 24.10.2 is available - Please consider updating your version to it
Loading