Nextflow workflow report

[ridiculous_dijkstra]

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

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

Command executed:

  change_sam_queries.py -Q -T 16 -t . calmd.bam variants.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/f7/b1bd6ddd8a022dec3ec3c30a0ec271

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 10:24:36 - 20-Jun-2022 10:39:17 (duration: 14m 41s)

  6 succeeded  

  0 cached  

  0 ignored  

  9 failed  

Nextflow command

nextflow run epidiverse/snp -profile test, docker

CPU-Hours

(a few seconds)

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

0cea4707-bd83-4d28-94c7-9ec0cd646d5d

Workflow repository

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

Workflow profile

test,

Nextflow version

version 20.07.1, build 5412 (24-07-2020 15:18 UTC)