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error trying to run on HPC #14

Closed Jane-Gibson closed 1 month ago

Jane-Gibson commented 3 months ago

Operating System

Other Linux (please specify below)

Other Linux

redhat

Workflow Version

v.1.1.0

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

run test data

${nextflow_exe_path} run epi2me-labs/wf-somatic-variation \ --bam_normal wf-somatic-variation-demo/demo_normal.bam \ --bam_tumor wf-somatic-variation-demo/demo_tumor.bam \ --ref wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set_chr20.fna \ --sv \ --snv \ --mod \ --sample_name SAMPLE \ --normal_min_coverage 0 \ --tumor_min_coverage 0 \ -profile apptainer \

Workflow Execution - CLI Execution Profile

singularity

What happened?

I'm running the somatic nextflow workflow via apptainer (singularity) on our HPC. It is failing at bam_ingress_normal:minimap2_ubam due to Relocation not allowed with starter-suid.

Is there a way to change our apptainer set up to allow this? or some option I should enable? thanks.

Relevant log output

ERROR ~ Error executing process > 'bam_ingress_normal:minimap2_ubam (1)'

Caused by:
  Process `bam_ingress_normal:minimap2_ubam (1)` terminated with an error exit status (255)

Command executed:

  samtools bam2fq -@ 1 -T 1  demo_normal.bam | minimap2 -y -t 1 -ax map-ont GCA_000001405.15_GRCh38_no_alt_analysis_set_chr20.fna -     | samtools sort -@ 1 --write-index -o SAMPLE.cram##idx##SAMPLE.cram.crai -O CRAM --reference GCA_000001405.15_GRCh38_no_alt_analysis_set_chr20.fna -

Command exit status:
  255

Command output:
  (empty)

Command error:
  FATAL:   Relocation not allowed with starter-suid

Work dir:
  /mainfs/scratch/jg/ONT_ANALYSES/NEXTFLOW/SOMATIC/work/7d/492f230af0c36d8f0ce2d7972b09d5

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Application activity log entry

No response

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

no

Other demo data information

No response

SamStudio8 commented 3 months ago

Hi @Jane-Gibson, rather fortuitously another user reported a similar issue yesterday: https://github.com/epi2me-labs/wf-human-variation/issues/161. It appeared to be related to how data partitions are mounted on their cluster. I would have a chat with your HPC administrator about this error in the first instance as they should hopefully be able to advise on the specifics of your HPC better than we can.

Jane-Gibson commented 3 months ago

ok, thanks. I will ask them and point them to the other issue.