[hhmake] -add_cons results in seq fault

soedinglab / hh-suite

Remote protein homology detection suite.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7

GNU General Public License v3.0

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[hhmake] -add_cons results in seq fault #252

Closed ksteczk closed 3 years ago

ksteczk commented 3 years ago

hhmake with option -add_cons results in seqfault, e.g.

ffindex_get pfam_a3m_oryg.ffdata pfam_a3m_oryg.ffindex PF00045.21|hhmake -i stdin -o stdout -neff 10 -add_cons output:

11:38:52.765 INFO: Reading HMM / multiple alignment from standard input ...

Segmentation fault

a3m files come from pfam 34 db from hh db repo. Without -add_cons it runs smoothly.

milot-mirdita commented 3 years ago

Did it work before? From What I can see combining Neff >= 0.999 and -add_cons should have basically always crashed. Not sure what the right fix is. Maybe ignoring -add_cons in hhmake completely as it prints the consensus sequence always anyway?

ksteczk commented 3 years ago

I just wanted to have a nice consensus sequence in the profile (not uniprot representative). The default consensus sequence is full of x'es and marks only the conserved residues. But I can live without that.

ghbillings commented 2 years ago

I'm hoping to re-open this; I'm running into what I assume is the same issue--I'm consistently getting segfaults when running hhblits with the -add_cons option. Not using -add_cons is a fine solution for us, but I'm hoping to save others the time it takes to figure out what's causing the segfaults.