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franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
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No metabat/samplename/cov/*.all.depth file and an empty concoct coverage_table.tsv #82

Closed slambrechts closed 1 year ago

slambrechts commented 3 years ago

Hi Francisco,

For 4 out of 43 samples, the /metabat/samplename/cov/*.all.depth files are missing, the concoct coverage_table.tsv file is empty, but the /maxbin/samplename/cov folder does contain depth files. Does that mean crossMap did not yield sufficient information to yield bins for these samples?

This should not interfere with the remaining metaGEM snakemake pipeline, right? Or should I remove these samples?

Kind regards, Sam

franciscozorrilla commented 3 years ago

Hi Sam,

I assume you are referring to crossMapSeries, correct? I find it strange that it fails to produce an output for 2 out of 3 binners. Without having seen the log files, I suspect that most likely the jobs were terminated prematurely or failed for some reason. Can you access the log files for those jobs? I think they will be quite large, feel free to attach one or two of them in your post.

Indeed, I believe that not having those binner input files will end up causing problems with the binRefine rule (only for those failed samples), as it expects 3 different bin sets but you will only be providing one. You can proceed with the pipeline for the remaining samples.

Apologies for the late response, I was away at a conference without my laptop 🤓 Best wishes, Francisco