Closed aclum closed 6 months ago
The only thing I can think of of in this instance is to use the latest version of checkm and update the docker image.
What version is Neha using?
From what I got from her is 1.2.1. But again, this was from a zip file I got of the files. There is no repo and no wdl wrapper.
The version is coded in a python script. https://github.com/microbiomedata/metaMAGs/blob/master/Docker/mbin_versions.py
versions = {
"mbin.py" : "0.5",
"metabat2" : "2.15",
"checkm-genome" : "1.2.1",
"gtdb-tk" : "2.1.1",
"hmmer" : "3.3.2",
"prodigal" : "2.6.3",
"pplacer" : "1.1.alpha19",
"fasttree" : "2.1.11",
"fastANI" : "1.33",
"mash" : "2.3",
"sqlite" : "3.39.2",
"Python" : "3.9.12"
}
Version 1.2.2 of checkm seems to be functional, but that would take us out of sync with JGI.
I noticed that none of our mags workflow results generate any bins, even projects for which we know the JGI processing generated mags (ie nmdc:wfmgan-11-585bp531.1, the JGI run of this data generated 27 medium and high quality mags, see img taxon oid 3300061644). I find errors in the call-mbin_nmdc stage 'ERROR: Models must be parsed before identifying HMM hits.' A quick search suggests an issue with the checkM installation https://github.com/Ecogenomics/CheckM/issues/280
This issue is not caught b/c the last process of the task completes correctly so we should also set pipefail to catch these types of problems going forward.
I can find 400 records on pscratch, this likely doesn't include deleted projects and the issue dates back to at least early August 2023 /pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags> grep 'ERROR: Models must be parsed before identifying HMM hits' */call-mbin_nmdc/execution/stdout | wc -l 600
cc @mbthornton-lbl