hhblits -i input.fasta -o /dev/null -ohhm PROFILE.hhm -n 2 -d uniclust30_2017_04/uniclust30_2017_04 -oa3m MSA.a3m
Segmentation fault is nearly always due to exhausted RAM..
i am facing the same error. kindly tell me the max RAM capacity should be to run hhblist?
The program itself requires negligible memory, so it comes down to database size you are using. I think you will need 64 Gb for any serious work, though you might get away with smaller RAM. It used to work with uniclust30 and 32 Gb, but those were earlier versions (maybe from 2016-2017). I think more recent uniclust30 versions require somewhere between 32-64 Gb.
Thnak you Mensur Dlakic . My ram capacity is 64Gb. As per your words i have maximum capacity but still the error remains the same.
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version 2.3.6
Very difficult to tell from the information your provided, but segmentation errors tend to be memory-related.
How much memory does your computer have? Is the input a single sequence in FASTA format? If not, are the sequences aligned? Are you using a precompiled binary (version?) or did you compile it locally? The more information you provide, the easier will be to troubleshoot it.