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nf-core / mag

Assembly and binning of metagenomes

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Centrifuge error - (ERR): mkfifo(/tmp/46.inpipe1) failed.

skrakau opened this issue · comments

commented

Description of the bug

I tried to run nf-core/mag with the test profile on a new compute cluster and got the following error:

-[nf-core/mag] Pipeline completed with errors-
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /mnt/lustre/groups/nahnsen/nahkr648/test/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'NFCORE_MAG:MAG:CENTRIFUGE (test_minigut-minigut_cf)'

Caused by:
  Process `NFCORE_MAG:MAG:CENTRIFUGE (test_minigut-minigut_cf)` terminated with an error exit status (17)

Command executed:

  centrifuge -x "minigut_cf"         -p 8         --report-file report.txt         -S results.txt         -1 "test_minigut_1.merged.fastq.gz" -2 "test_minigut_2.merged.fastq.gz"
  centrifuge-kreport -x "minigut_cf" results.txt > test_minigut.centrifuge_kreport.txt
  cat results.txt | cut -f 1,3 > results.krona

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_MAG:MAG:CENTRIFUGE":
      centrifuge: $(centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
  END_VERSIONS

Command exit status:
  17

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
  WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  (ERR): mkfifo(/tmp/46.inpipe1) failed.
  Exiting now ...

Work dir:
  /mnt/lustre/groups/nahnsen/nahkr648/test/work/56/78d3c43078646a260420d4b2e1a5b6

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

The .command.log and .command.err contain

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
WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
(ERR): mkfifo(/tmp/46.inpipe1) failed.
Exiting now ...

I guess it is related to the Centrifuge problem with the tmp dir as described in nf-core/taxprofiler#422 (and solved in nf-core/taxprofiler#444).
Just wanted to mention it here, in case it is still relevant.

Command used and terminal output

nextflow run nf-core/mag -r 2.5.4 -profile test -c myM3C.config --outdir results -resume


### Relevant files

_No response_

### System information

- Nextflow version 23.10.1
- HPC
- Slurm
- Singularity
- nf-core/mag 2.5.4
commented

Yes, before I went travelling I was trying to address using the more recent container that allows us to fix this, this but it appears I have to replace the entire centrifuge workflow (can't mix and match local/non local modules 😞

commented

Yes, before I went travelling I was trying to address using the more recent container that allows us to fix this, this but it appears I have to replace the entire centrifuge workflow (can't mix and match local/non local modules 😞

Oh no 😞