Skip to content
nf-core CI

Merge pull request #1754 from FriederikeHanssen/fixtest #6626

Sign in to view logs

Merge pull request #1754 from FriederikeHanssen/fixtest

Merge pull request #1754 from FriederikeHanssen/fixtest #6626

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

9 tests run, 5 passed, 0 skipped, 4 failed.

Annotations

Check failure on line 1 in Test pipeline when starting from markduplicates

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline when starting from markduplicates.Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --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` [sad_goldberg] DSL2 - revision: 3954909713

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek 3.5.0
------------------------------------------------------
Input/output options
  input                     : /home/runner/work/sarek/sarek/tests/csv/3.0/mapped_single_cram.csv
  step                      : markduplicates
  outdir                    : /home/runner/work/sarek/sarek/~/tests/9648efead9946a3085d761d324a1ef0/output

Main options
  split_fastq               : 0
  intervals                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.interval_list
  skip_tools                : markduplicates

Annotation
  bcftools_annotations      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz
  bcftools_annotations_tbi  : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi
  bcftools_header_lines     : /home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt

General reference genome options
  igenomes_base             : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Reference genome options
  genome                    : testdata.nf-core.sarek
  dbsnp                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi
  dbsnp_vqsr                : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
  dict                      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.fasta
  fasta_fai                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.fasta.fai
  germline_resource         : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz
  germline_resource_tbi     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi
  known_indels              : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
  known_indels_tbi          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi
  known_indels_vqsr         : --resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz
  ngscheckmate_bed          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed
  sentieon_dnascope_model   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
  snpeff_cache              : null
  snpeff_db                 : WBcel235.105
  vep_cache                 : null
  vep_cache_version         : 113
  vep_genome                : WBcel235
  vep_species               : caenorhabditis_elegans

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
  modules_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Core Nextflow options
  runName                   : sad_goldberg
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/9648efead9946a3085d761d324a1ef0
  workDir                   : /home/runner/work/sarek/sarek/~/tests/9648efead9946a3085d761d324a1ef0/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,conda
  configFiles               : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* 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/9648efead9946a3085d761d324a1ef0/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/9648efead9946a3085d761d324a1ef0/work/conda/environment-d2d82a1cc7858810940ff84273e57b63]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/9648efead9946a3085d761d324a1ef0/work/conda/environment-873a3583ebab040412cb72c07ed757ab]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/9648efead9946a3085d761d324a1ef0/work/conda/environment-57cd7e91fe23a8ceb488416c37dae89b]
[f4/6a8877] 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/9648efead9946a3085d761d324a1ef0/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/9648efead9946a3085d761d324a1ef0/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/9648efead9946a3085d761d324a1ef0/meta/nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-
Join mismatch for the following entries: key=[patient:test, sample:test, sex:NA, status:0, id:test, data_type:cram] values=


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 recalibration

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline when starting from recalibration.Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step recalibrate --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` [silly_sammet] DSL2 - revision: 3954909713

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek 3.5.0
------------------------------------------------------
Input/output options
  input                     : /home/runner/work/sarek/sarek/tests/csv/3.0/prepare_recalibration_single_bam.csv
  step                      : recalibrate
  outdir                    : /home/runner/work/sarek/sarek/~/tests/5b934a25029e2d5b4ee9d632a85a7722/output

Main options
  split_fastq               : 0
  intervals                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.interval_list

Annotation
  bcftools_annotations      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz
  bcftools_annotations_tbi  : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi
  bcftools_header_lines     : /home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt

General reference genome options
  igenomes_base             : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Reference genome options
  genome                    : testdata.nf-core.sarek
  dbsnp                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi
  dbsnp_vqsr                : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
  dict                      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.fasta
  fasta_fai                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.fasta.fai
  germline_resource         : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz
  germline_resource_tbi     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi
  known_indels              : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
  known_indels_tbi          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi
  known_indels_vqsr         : --resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz
  ngscheckmate_bed          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed
  sentieon_dnascope_model   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
  snpeff_cache              : null
  snpeff_db                 : WBcel235.105
  vep_cache                 : null
  vep_cache_version         : 113
  vep_genome                : WBcel235
  vep_species               : caenorhabditis_elegans

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
  modules_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Core Nextflow options
  runName                   : silly_sammet
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/5b934a25029e2d5b4ee9d632a85a7722
  workDir                   : /home/runner/work/sarek/sarek/~/tests/5b934a25029e2d5b4ee9d632a85a7722/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,conda
  configFiles               : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* 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/5b934a25029e2d5b4ee9d632a85a7722/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/5b934a25029e2d5b4ee9d632a85a7722/work/conda/environment-d2d82a1cc7858810940ff84273e57b63]
[b2/b04d61] 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/5b934a25029e2d5b4ee9d632a85a7722/work/conda/environment-497b0f18c811c5671b5e17e0034188ed]
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (1)'

Caused by:
  java.nio.channels.OverlappingFileLockException



 -- Check '/home/runner/work/sarek/sarek/~/tests/5b934a25029e2d5b4ee9d632a85a7722/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/5b934a25029e2d5b4ee9d632a85a7722/meta/nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-
Nextflow stderr:

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

Check failure on line 1 in Test pipeline

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline.Run with profile test | --tools controlfreec | somatic 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.04.2
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [wise_almeida] DSL2 - revision: 3954909713

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek 3.5.0
------------------------------------------------------
Input/output options
  input                     : /home/runner/work/sarek/sarek/tests/csv/3.0/recalibrated_somatic.csv
  step                      : variant_calling
  outdir                    : /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/output

Main options
  split_fastq               : 0
  intervals                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed
  wes                       : true
  tools                     : controlfreec

Annotation
  bcftools_annotations      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz
  bcftools_annotations_tbi  : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi
  bcftools_header_lines     : /home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt

General reference genome options
  igenomes_base             : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Reference genome options
  genome                    : testdata.nf-core.sarek
  chr_dir                   : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz
  dbsnp                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz
  dbsnp_tbi                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi
  dbsnp_vqsr                : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
  dict                      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta
  fasta_fai                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai
  germline_resource         : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz
  germline_resource_tbi     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi
  known_indels              : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
  known_indels_tbi          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi
  known_indels_vqsr         : --resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz
  ngscheckmate_bed          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed
  sentieon_dnascope_model   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
  snpeff_cache              : null
  snpeff_db                 : WBcel235.105
  vep_cache                 : null
  vep_cache_version         : 113
  vep_genome                : WBcel235
  vep_species               : caenorhabditis_elegans

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
  modules_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Core Nextflow options
  runName                   : wise_almeida
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32
  workDir                   : /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,conda
  configFiles               : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* 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/d46f6304d77366be7c2f91242287e32/work/conda/gawk-f9b4f646bf1b67e52890543d27cb2f27]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/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/d46f6304d77366be7c2f91242287e32/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/d46f6304d77366be7c2f91242287e32/work/conda/environment-57cd7e91fe23a8ceb488416c37dae89b]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/work/conda/environment-873a3583ebab040412cb72c07ed757ab]
[20/a09dc3] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (multi_intervals.bed)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_TUMOR:SAMTOOLS_MPILEUP (1)'

Caused by:
  java.nio.channels.OverlappingFileLockException



 -- Check '/home/runner/work/sarek/sarek/~/tests/d46f6304d77366be7c2f91242287e32/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/d46f6304d77366be7c2f91242287e32/meta/nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-
Nextflow stderr:

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

Check failure on line 1 in Test pipeline

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

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

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.04.2
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [elated_visvesvaraya] DSL2 - revision: 3954909713

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek 3.5.0
------------------------------------------------------
Input/output options
  input                     : /home/runner/work/sarek/sarek/tests/csv/3.0/recalibrated_somatic.csv
  step                      : variant_calling
  outdir                    : /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/output

Main options
  split_fastq               : 0
  intervals                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed
  no_intervals              : true
  tools                     : manta,strelka

Annotation
  bcftools_annotations      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz
  bcftools_annotations_tbi  : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi
  bcftools_header_lines     : /home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt

General reference genome options
  igenomes_base             : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Reference genome options
  genome                    : testdata.nf-core.sarek
  dbsnp                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi
  dbsnp_vqsr                : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
  dict                      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta
  fasta_fai                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai
  germline_resource         : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz
  germline_resource_tbi     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi
  known_indels              : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
  known_indels_tbi          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi
  known_indels_vqsr         : --resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz
  ngscheckmate_bed          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed
  sentieon_dnascope_model   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
  snpeff_cache              : null
  snpeff_db                 : WBcel235.105
  vep_cache                 : null
  vep_cache_version         : 113
  vep_genome                : WBcel235
  vep_species               : caenorhabditis_elegans

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
  modules_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Core Nextflow options
  runName                   : elated_visvesvaraya
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9
  workDir                   : /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,conda
  configFiles               : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* 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/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/environment-497b0f18c811c5671b5e17e0034188ed]
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/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/environment-86f8fc4b934d0b08515f88ef4592bd1f]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_single_strelka/../../../modules/nf-core/strelka/germline/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/environment-438a505d7b44a08705c858f9ad6e02ce]
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/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/environment-873a3583ebab040412cb72c07ed757ab]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/work/conda/environment-57cd7e91fe23a8ceb488416c37dae89b]
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (1)'

Caused by:
  java.nio.channels.OverlappingFileLockException



 -- Check '/home/runner/work/sarek/sarek/~/tests/d83ad9e6ce5149f25ccf62ff7c16f9a9/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/d83ad9e6ce5149f25ccf62ff7c16f9a9/meta/nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-
Join mismatch for the following entries: key=[id:sample4_vs_sample3, normal_id:sample3, patient:test3, sex:XX, tumor_id:sample4] values=


Nextflow stderr:

Nextflow 24.10.2 is available - Please consider updating your version to it
View more details on GitHub Actions