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GTDBTK_CLASSIFYWF process does not put the summary.tsv file in the output directory #637
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Hi @jhayer ! Thanks for the report. The empty columns in the file can be valid behaviour sometimes... It looks like gtdbtk did not complete exactly, but if the pipeline didn't fail, possibly in a way that is valid to gtdbtk. Could you please share the |
I'm also having some issues with GTDBTK, which I've detailed in another issue: #641 In my case, it looks like the tool was only run on one sample (of several). I did get the |
@jhayer any chance you still have those log files? Otherwise it will be hard to investigate further. |
Ok, I am sorry, the But I am still wondering why the |
I'm not 💯 sure still (sorry, I've been on parental leave then my son was sick) In checking/testing another GTDB Tk pull request, I noticed that in some cases, if GTDB-Tk doesn't find any hits it just doesn't produce a output file that can be parsed. For those samples that don't have a I've just had a thought how I can maybe demonstrate this, but please check in the meantime |
I've found the issue @jhayer !!! This is apparently a three year old bug that no-one picked up on 😅 |
Uff, sorry for that, my bad! |
Sorry this took such a long time for such a small fix @jhayer ! Thanks for reporting! |
Description of the bug
Hi,
We have been running nf-core/mag, 2 different versions (2.5.1 and 3.0.1) and we end up with missing files in the GTDB-Tk output directory. The summary.tsv files are in the work directories, but it seems that they are not moved to the main output dir.
The files that are present in the output directories for GTDB-Tk are the following:
In the corresponding work dir, I have those files:
This problem leads to another problem, being that then the main gtdbtk summary has no classification for none of the samples:
Do you have an idea of what could go wrong here?
Thanks :-)
Command used and terminal output
nextflow run nf-core/mag -r 3.0.1 -profile singularity -resume -params-file nf-params.json -c local.config
Relevant files
file nf-params.json is:
file local.config
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