variant calling failed at concat_refined_snp step

[samuelecancellieri]

Operating System

Other Linux (please specify below)

Other Linux

Red Hat Enterprise Linux 9.4

Workflow Version

2.2.3

Workflow Execution

Command line (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-human-variation --bam /storage/sahuarea/samuele_cancellieri/fei_ffpes/nanopore_dna-seq/LYM1/20240510_1453_P2S-00885-A_PAS09250_ca256177/bam_pass/ --out_dir lym1_all_variant_calling --depth_intervals --sv --snp --cnv --sample_name lym1_pass --ref /storage/sahuarea/samuele_cancellieri/reference_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna --bam_min_coverage 0 -resume -profile singularity

Workflow Execution - CLI Execution Profile

singularity

What happened?

the pipeline stops and report an error at "concat_refined_snp" step
command.run.log

Relevant log output

ERROR ~ Error executing process > 'concat_refined_snp'

Caused by:
  Process `concat_refined_snp` terminated with an error exit status (255)

Command executed:

  bcftools concat --threads 1 -O u vcfs/*.vcf.gz | bcftools sort -O z - > "lym1_pass.wf_snp.vcf.gz"
  tabix -p vcf lym1_pass.wf_snp.vcf.gz

Command exit status:
  255

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Checking the headers and starting positions of 25 files
  mkdtemp(/storage/sahuarea/samuele_cancellieri/general_tmp/bcftools.FFZZJf) failed: No such file or directory
  Concatenating vcfs/lym1_pass.chr1.wf_snp.vcf.gz       0.001603 seconds
  Concatenating vcfs/lym1_pass.chr10.wf_snp.vcf.gz      0.001012 seconds
  Concatenating vcfs/lym1_pass.chr11.wf_snp.vcf.gz      0.000834 seconds
  Concatenating vcfs/lym1_pass.chr12.wf_snp.vcf.gz      0.000814 seconds
  Concatenating vcfs/lym1_pass.chr13.wf_snp.vcf.gz      0.000840 seconds
  Concatenating vcfs/lym1_pass.chr14.wf_snp.vcf.gz      0.000808 seconds
  Concatenating vcfs/lym1_pass.chr15.wf_snp.vcf.gz      0.000787 seconds
  Concatenating vcfs/lym1_pass.chr16.wf_snp.vcf.gz      0.000935 seconds
  Concatenating vcfs/lym1_pass.chr17.wf_snp.vcf.gz      0.000711 seconds
  Concatenating vcfs/lym1_pass.chr18.wf_snp.vcf.gz      0.000807 seconds
  Concatenating vcfs/lym1_pass.chr19.wf_snp.vcf.gz      0.000745 seconds
  Concatenating vcfs/lym1_pass.chr2.wf_snp.vcf.gz

Work dir:
  /storage/sahuarea/samuele_cancellieri/fei_ffpes/nanopore_dna-seq/work/b6/7c496e917db333fa1e7d83b81f0ae6

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

other (please describe below)

Other demo data information

didn't try, but with skipping the snp calling, the pipeline completes without any problem

[SamStudio8]

@samuelecancellieri It looks as though the Nextflow process is unable to write to your assigned TMPDIR.

mkdtemp(/storage/sahuarea/samuele_cancellieri/general_tmp/bcftools.FFZZJf) failed: No such file or directory

You should be able to either:

• Unset TMPDIR when calling Nextflow to prevent this variable bleeding into your containers (which will then use their own TMP)
• Ensure you bind your TMPDIR to your Singularity containers by setting --bind <YOUR TMPDIR> to the containerOptions directive (https://www.nextflow.io/docs/latest/process.html#containeroptions)