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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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SPAdes memory limit #150

Closed aleixop closed 3 years ago

aleixop commented 3 years ago

Hi, thanks for this great tool! Is there a way to increase the 20GB memory limit (-m 20) in the SPAdes step? I have 120GB of RAM available but jobs keep crashing due to this limit. Thanks!

kbseah commented 3 years ago

At the moment we didn't implement a way to change this from the phyloFlash command line, but you can manually edit the phyloFlash.pl script at line 1585 (I think you've already found it) to a higher value. That's the only place the parameter appears, if i remember correctly

aleixop commented 3 years ago

Okay, thanks a lot!