Command 'ps' required by nextflow to collect task metrics cannot be found

[chenhijy]

Description of the bug

I had successfully been running nf-pangenome on AWS EC2 using tibanna and a snakemake pipeline, but today I started getting this error irrespective of whether I set -profile to singularity, docker, or conda

I'm reading online that maybe ps needs to be explicitly installed into nf-pangenome's container. Can anyone help with this?

The command in the snakemake rule is

nextflow run nf-core/pangenome \
    --input panSNCombined.fa.gz \
    --n_haplotypes 14 \
    --outdir <outdir> \
    --communities true \
    -profile singularity \
    -c <customNfConfig.json> \
    -process.echo

This is the error I get

ERROR ~ Error executing process > 'NFCORE_PANGENOME:PANGENOME:INPUT_CHECK:SAMTOOLS_FAIDX (panSNCombined.fa.gz)'

Caused by:
  Process `NFCORE_PANGENOME:PANGENOME:INPUT_CHECK:SAMTOOLS_FAIDX (panSNCombined.fa.gz)` terminated with an error exit status (1)


Command executed:

  samtools \
      faidx \
     panSNCombined.fa.gz \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_PANGENOME:PANGENOME:INPUT_CHECK:SAMTOOLS_FAIDX":
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Command 'ps' required by nextflow to collect task metrics cannot be found

Command used and terminal output

No response

Relevant files

No response

System information

Docker version 23.0.3, build 3e7cbfd
Python 3.8.10
pip 20.0.2
tibanna awsf3 version 3.3.1
cwltool version 3.1.20211103193132
cromwell version 35 for WDL draft2
cromwell version 53.1 for WDL v1.0
singularity-ce version 3.10.4-focal
goofys version 0.24.0-45b8d78375af1b24604439d2e60c567654bcdf88
snakemake 7.28.3
nf-core/pangenome 1.1.2-gaf6d1dd
 N E X T F L O W   ~  version 24.04.4
r6a.32xlarge EC2 instance

[subwaystation]

I have no idea, but I am asking around.

[chenhijy]

We think we solved the issue. We had added a # comment to the snakemake shell directive that seems to have been causing unpredictable behavior with the nf-pangenome container (i.e. various utilities and tools -- such as ps, samtools, etc -- were unavailable). After removing this, the pipeline started working again.

[subwaystation]

Great, thanks for letting me know!