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microbiomedata / metaT

Metatranscriptomics workflow
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rfam failing for small sample files #35

Closed mflynn-lanl closed 4 days ago

mflynn-lanl commented 2 weeks ago

the task rfam.run is failing for small sample files. This is because the _rfam.tbl is empty and so the grep command returns no results. Since we have set -euo pipefail this results in the task failing.

mhuntemann commented 2 weeks ago

Hi, Maybe you guys are not running the latest version of the script from the original pipeline. It has a check for that which got added in May last year. You can find the latest version here: https://code.jgi.doe.gov/img/img-pipelines/img-annotation-pipeline/-/blob/main/bin/structural_annotation/cmsearch_rfams.sh?ref_type=heads

mflynn-lanl commented 1 week ago

@mhuntemann, where do we use that script? I don't see it used in rfam.wdl

ssarrafan commented 4 days ago

@mflynn-lanl @vlilanl looks like you're waiting to hear back on more information. I'll move this to the new sprint. FYI @aclum

aclum commented 4 days ago

@mflynn-lanl The problem is that metatranscriptome annotation, what is in this repo, is out of sync. the annotation repo does have this workaround, see https://github.com/microbiomedata/mg_annotation/blob/master/rfam.wdl. Closing this as won't fix as @kaijli is working on getting everything synchronized with the latest code.

cc @vlilanl