mmseqs2 prefilter failed: No k-mer could be extracted for the database genomad_db/genomad_db about genomad

[apcamargo]

Hi @haleyhallowell. I don't think I've seen this error before. Do you still get it if you remove short sequences? Could you share the input with me?

[haleyhallowell]

Hey! Sure, I can share with you; it is attached! I'm currently waiting on another run to go through the HPC queue. I noticed that when i used pip install genomad that i had to manually install prodigal-gv and mmseqs2, so i made a new environment using a conda install. ill update you once that goes through!
final_vOTUs_numbered.txt.zip

Not sure on the short sequences, nothing should be that short as i filter out <2000bp

[haleyhallowell]

Hi! Just wanted to let you know i got it working -- seems like it was the weird install with pip i mentioned above that made it throw this error. Conda install the second time got it working. Thanks!

[apcamargo]

Thanks for letting me know! I'll close the issue.

Maybe it was a problem with the MMseqs2 version? The latest versions of geNomad are only compatible with version 14-7e284.