[Bug]: Process `pipeline:getVersions` terminated with an error exit status (141)

[QGouil]

What happened?

The command samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt exits with code 141 and kills the pipeline. This is with head v8.22 Adding || true at the end of the line keeps the pipefail happy.

In addition, could there also be a conflict between unix last and bioconda last when fetching the versions? The correct command seems to be lastal --version rather than last --version.

Operating System

ubuntu 18.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - Execution Profile

Conda

Workflow Version

v0.2.5

Relevant log output

Error executing process > 'pipeline:getVersions'

Caused by:
  Process `pipeline:getVersions` terminated with an error exit status (141)

Command executed:

  medaka --version | sed 's/ /,/' >> versions.txt
  minimap2 --version | sed 's/^/minimap2,/' >> versions.txt
  samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  seqkit version | sed 's/ /,/' >> versions.txt
  trycycler --version | sed 's/ /,/' >> versions.txt
  porechop --version | sed 's/^/porechop,/'  >> versions.txt
  bedtools --version | sed 's/ /,/' >> versions.txt
  canu -version | sed 's/ /,/' >> versions.txt
  fastcat --version | sed 's/^/fastcat,/' >> versions.txt
  last --version | sed 's/ /,/' >> versions.txt
  rasusa --version | sed 's/ /,/' >> versions.txt
  python -c "import spoa; print(spoa.__version__)" | sed 's/^/spoa,/'  >> versions.txt

Command exit status:
  141

Command output:
  (empty)

[sarahjeeeze]

Hi, This should be fixed in the latest version of the workflow.

[sarahjeeeze]

Closing as issue resolved.