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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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minimus2,spend 5 days! #593

Closed luozhy88 closed 1 year ago

luozhy88 commented 1 year ago

It took me 5 days to run minimus2, which took so much time, but it wasn't finished yet for 40 samples. my memory is 1T! SqueezeMeta.pl -m merged -p PJ_mergedv2 -s test.sample.rm_host -f rm_host --nopfam --nobin -t 100 image

fpusan commented 1 year ago

Yes, minimus2 scales notably bad with the number of samples, this has been discussed in several other issues. We have been looking for alternative software for performing this step, but as of today we have no better alternative. You are probably better off trying a coassembly using megahit (maybe with 1T memory it will work) or using the sequential mode.

fpusan commented 1 year ago

Closing due to lack of activity, feel free to reopen