search

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
189 stars 41 forks source link

refined_bins output remains empty after successful binRefine step #143

Closed kunaljaani closed 8 months ago

kunaljaani commented 9 months ago

Hi Francisco,

While running bash metaGEM.sh -t binRefine -j 2 -c 24 -m 150 -h 24 -l command ends without any error. But surprisingly, the refined_bins output remains empty. Especially, the metawrap_50_10_bins directory which should ideally have refined bins, and also metawrap_50_10_bins.contigs remain empty. I also tried rerunning the pipeline using the toy dataset to find the problem but wasn't successful. Could you please suggest a fix?

Thank you Kunal binrefin

franciscozorrilla commented 9 months ago

Hi Kunal, based on this information it seems like probably some file path is pointing in the wrong direction. Please inspect your config.yaml file to check that they are properly configured. If you are using a tmp dir, check if the metawrap output is present there. Also, have a look at the assembly of your sample, is it large/good enough to assemble MAGs from?

franciscozorrilla commented 8 months ago

Closing due to inactivity, please feel free to re-open if you have more questions or the issue persists.