Nextflow workflow report

[distracted_bohr]

Error executing process > 'SNPS:masking (sample1 - clustering)'

Caused by:
  Process `SNPS:masking (sample1 - clustering)` terminated with an error exit status (1)

Command executed:

  change_sam_queries.py -Q -T 16 -t . -G calmd.bam clustering.bam || exit $?
  find -mindepth 1 -maxdepth 1 -type d -exec rm -r {} \;

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/sr320/.nextflow/assets/epidiverse/snp/bin/change_sam_queries.py", line 68, in 
      import pysam
  ImportError: No module named pysam

Work dir:
  /home/shared/8TB_HDD_01/sr320/github/paper-oly-mbdbs-gen/code/work/87/1c1f26fb97ea2d12fc85423262c591

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Run times

20-Jun-2022 09:55:09 - 20-Jun-2022 09:55:28 (duration: 18.8s)

  6 succeeded  

  0 cached  

  0 ignored  

  8 failed  

Nextflow command

nextflow run epidiverse/snp -profile test, docker

CPU-Hours

0.1 (79.7% failed)

Launch directory

/home/shared/8TB_HDD_01/sr320/github/paper-oly-mbdbs-gen/code

Work directory

/home/shared/8TB_HDD_01/sr320/github/paper-oly-mbdbs-gen/code/work

Project directory

/home/sr320/.nextflow/assets/epidiverse/snp

Script name

main.nf

Script ID

b0e299ed332648922c66d8a020a05bca

Workflow session

a8746d6d-fb59-42da-8d56-9e8ed48516ed

Workflow repository

https://github.com/epidiverse/snp, revision master (commit hash 9c814703c690c2ade21c4586b36159940e092a4e)

Workflow profile

test,

Nextflow version

version 22.04.3, build 5703 (18-05-2022 19:22 UTC)