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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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metaWrap binning inquiry metabat2 maxbin2 concoct #547

Open lcamVz opened 4 months ago

lcamVz commented 4 months ago

I've been running metawrap binning with the the 3 tools while metabat2 ran perfecttly with maxbin2 and concoct it ran 168 hours and did not finished I checked for the maxbin2 and I found the maxbin2_out folder inside the work_files did maxbin2 actually finished because I didnt get the final output folder like the metabata2_bins, or is it it waits for concoct to run to actually havr the three expecte folders in the bin folder? Has anyone experiences this before?

yqy6611 commented 4 months ago

Don't use that metawrap-mg package. Totally outdated. Prepare a cleaner conda environment with python 3 and manually install those dependencies except for prokka and salmon can solve majority problems. For some small auxiliary python 2 scripts we can prepare another python 2 environment and redirect python interpreter in those scripts. Same for prokka and salmon, prepare separate environments for each of them and redirect the locations in scripts.

DCossey commented 2 months ago

I got the same issue with output directory for maxbin inside my work_files and what appears to be the non-binned files in the subdirectory for each binner. Have you managed to resolve this issue?