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apcamargo / genomad

geNomad: Identification of mobile genetic elements
https://portal.nersc.gov/genomad/
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genomad hangs #80

Closed erinyoung closed 3 months ago

erinyoung commented 3 months ago

Hi! I have a strange use case.

I'm trying to run genomad in gitpod - which has very low computational options.

I get to this step where it hangs:

 => => # [20:51:22] Proteins predicted with pyrodigal-gv were written to                                                                                      
 => => #            GCA_025259185.1_ASM2525918v1_genomic_proteins.faa.

Is there anything I can do to get it to... not hang?

apcamargo commented 3 months ago

Hi @erinyoung

If MMseqs2 is hanging, you can try to increase the number of splits (e.g. -s 16).

Other than that, you can take a look at some tips here: https://portal.nersc.gov/genomad/faq.html

erinyoung commented 3 months ago

Perfect! Thank you!