nf-core / nf-core/sarek

Pipeline interrupts immediatly after launching

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bug
Dominant language
Nextflow
Stars
603
Forks
548
Avg merge
2d 18h
Merged PRs (30d)
1

Description

Description of the bug

The pipeline interrupts at the very beginning with an error message when running on HPC. However, when running on a local machine, it completes successfully.

Command used and terminal output
nextflow run nf-core/sarek -r 3.5.0 -c /shared/apps/nextflow/nextflow.config -params-file /path/to/nf-param2a.json -work-dir /path/to/work_dir --outdir /path/to/out_dir -with-report -with-trace -with-timeline
Error message:
ERROR ~ Error executing process > 'NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr2H_1_1-330629716)'

Caused by:
  Process `NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr2H_1_1-330629716)` terminated for an unknown reason -- Likely it has been terminated by the external system


Command executed:

  bgzip  --threads 1 -c  chr2H_1_1-330629716.bed > chr2H_1_1-330629716.bed.gz
  tabix --threads 1  chr2H_1_1-330629716.bed.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT":
      tabix: $(echo $(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*$//')
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/htslib:1.20--h5efdd21_2' locally
  1.20--h5efdd21_2: Pulling from biocontainers/htslib
  Digest: sha256:8493a05024391d1242a4c4e4ee88a47d43c266a2da1909f2ff0bf9867f5187ee
  Status: Image is up to date for quay.io/biocontainers/htslib:1.20--h5efdd21_2

Work dir:
  /svevo/davide_tmp/work_dir/42/22a673ae4b0b4f2c3b9959f70de3c9

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

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

No response

System information

Nextflow version: N E X T F L O W ~ version 24.04.2
Hardware: HPC
Executor: slurm
Container engine: Docker
Os: Linux
nf-core/sarek 3.5.0

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the referenced .nextflow.log and the work directory's .command.out for the TABIX_BGZIPTABIX_INTERVAL_SPLIT process. Compare the Slurm and Docker execution details with the successful local run, then identify why the external system terminates the process. Done means the HPC pipeline completes this process reliably or the execution requirement is documented.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, linux
Domain
bioinformatics, infrastructure
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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