Jan Kosinski
Jan Kosinski
I also have this issue: ## Expected Behavior hhblits does not crash on this sequence: ``` >Q13838_DX39B_HUMAN MAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIEQTR ``` and using uniclust30_2018_08 database. ## Current Behavior hhblits crashes with the...
> Janek, I ran your command /opt/hhsuite/bin/hhblits -i query-kosinski.fst -cpu 100 -oa3m query-kosinski.a3m -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /db/hh/UniRef30_2020_06 -d /home/db/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt >...
> > Janek, I ran your command /opt/hhsuite/bin/hhblits -i query-kosinski.fst -cpu 100 -oa3m query-kosinski.a3m -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /db/hh/UniRef30_2020_06 -d /home/db/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt...
> > Hold on, or is the UniRef30_2020_06 basically updated version of uniclust30_2018_08? > > I believe yes - they are calling it uniclust but the files are named Uniref30......
[UniRef30_2021_03](http://gwdu111.gwdg.de/~compbiol/uniclust/2021_03/) gives similar errors just on different sequences.
> The multi-database feature of HH-suite seems the be the problem. If you search against the Uniref30 and the BFD separately it works without crashing. Please do not use this...
Well, I haven't edited the code to enable this. I guess the easiest would have to run hhblits twice and combine the alignments into one file named bfd_uniclust_hits.a3m, but I...
I got it too, and for me this worked: ``` conda (or mamba) update --all -c pytorch ```
The problem is this call: ``` label_asym_id = self._get_label_asym_id(entity_id) ``` of this function: ``` def _get_label_asym_id(self, entity_id): # Convert a positive integer into a chain ID # Goes A to...
Yes, in the case of the PDB the label_asym_id could take chain id. At least, this is what ColabFold/AlphaFold with custom templates expect. I think some molecular viewers would also...