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nf-core / pathogensurveillance

Surveillance of pathogens using population genomics and sequencing
https://nf-co.re/pathogensurveillance
MIT License
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sourmash not found #12

Closed cahuparo closed 8 months ago

cahuparo commented 1 year ago

Description of the bug

When I ran the test dataset, I got the error below.

Aug-09 21:12:34.834 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_PLANTPATHSURVEIL:PLANTPATHSURVEIL:ASSIGN_REFERENCES:SOURMASH_SKETCH_GENOME (22_331_assembly)'

Caused by:
  Process `NFCORE_PLANTPATHSURVEIL:PLANTPATHSURVEIL:ASSIGN_REFERENCES:SOURMASH_SKETCH_GENOME (22_331_assembly)` terminated with an error exit status (127)

Command executed:

  sourmash sketch \
      dna --param-string 'scaled=1000,k=21,k=31,k=51' \
      --merge '22_331_assembly' \
      --output '22_331_assembly.sig' \
      reference-22-331.fna

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_PLANTPATHSURVEIL:PLANTPATHSURVEIL:ASSIGN_REFERENCES:SOURMASH_SKETCH_GENOME":
      sourmash: $(echo $(sourmash --version 2>&1) | sed 's/^sourmash //' )
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: sourmash: command not found

Work dir:
  /nfs7/BPP/Chang_Lab/paradarc/nf_brady_N120/scripts/nf-core-plantpathsurveil/work/a2/480383e27aa8caca0e987eaf408c31

If I add the path to the sourmash executable installed in my conda env works no problem. So this maybe an issue with my conda installation or with the way the pipeline calls the sourmash conda.

Command used and terminal output

nextflow run main.nf -profile test,mamba --outdir test -resume

Relevant files

No response

System information

No response

zachary-foster commented 1 year ago

probably a conda/mamba issue. Is this still a problem?