czbiohub-sf / nf-predictorthologs

*de novo* orthologous gene predictions from bam + bed or fasta/fastq data
MIT License
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Conda unzip incompatible with NCBI's taxdmp.zip #14

Closed olgabot closed 4 years ago

olgabot commented 4 years ago

Using conda's unzip causes this error:

Error executing process > 'diamond_prepare_taxa (taxdmp)'
Caused by:
  Process `diamond_prepare_taxa (taxdmp)` terminated with an error exit status (9)
Command executed:
  unzip taxdmp.zip
Command exit status:
  9
Command output:
  Archive:  taxdmp.zip
Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
    End-of-central-directory signature not found.  Either this file is not
    a zipfile, or it constitutes one disk of a multi-part archive.  In the
    latter case the central directory and zipfile comment will be found on
    the last disk(s) of this archive.
  unzip:  cannot find zipfile directory in one of taxdmp.zip or
          taxdmp.zip.zip, and cannot find taxdmp.zip.ZIP, period.
Work dir:
  /home/phoenix/code/nf-predictorthologs/work/3c/c7ceff90ab63d1d82189dd9fbfac13
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Replace with apt-get's unzip

olgabot commented 4 years ago

Thanks @phoenixAja for the example!

olgabot commented 4 years ago

Closed by https://github.com/czbiohub/nf-predictorthologs/pull/34