replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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new splitfasta requires 4 CPUs -- and will not run with --cpus 1 --max_cpus 1 #130

Closed RaverJay closed 3 years ago

RaverJay commented 3 years ago

This should also be usable with 1 cpu (related: #122)

[d5/65e471] process > get_fasta                                     [100%] 1 of 1, cached: 1 ✔
[f7/f37eb3] process > split_fasta                                   [100%] 1 of 1, failed: 1
[-        ] process > determine_lineage_wf:pangolin                 -
[-        ] process > determine_mutations_wf:nextclade              -
[-        ] process > genome_quality_wf:president                   -
[-        ] process > genome_quality_wf:seqrs                       -
[-        ] process > rki_report_wf:rki_report                      -
[-        ] process > create_summary_report_wf:summary_report_fasta -
Error executing process > 'split_fasta'

Caused by:
  Process requirement exceed available CPUs -- req: 4; avail: 1

Command executed:

  mkdir -p split_fasta
     split_fasta.py SARSCoV2.fasta

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /data/mahlzeitlocal/sebastian/porecov_dev/work/nextflow-poreCov-ya86gul/f7/f37eb38dc21d18b9654ed3b8d05a4e

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
replikation commented 3 years ago

yes agree --fasta should work with one thread