hhfilter 65535 sequence limit about hh-suite HOT 7 CLOSED

@alquraishi, you are right, this should definitely be documented. We are very sorry for the inconvenience.

from hh-suite.

I got a similar issue with HHblits. It would be great to pass this threshold sometimes.

from hh-suite.

Hello,

you are right. There should be a warning. And there was a warning, but it was not reachable in the code. This should be fixed now.

hhfilter -i huge.a3m -o test.a3m
- 16:35:00.940 INFO: Input file = huge.a3m

- 16:35:00.940 INFO: Output file = test.a3m

- 16:35:01.376 WARNING: Maximum number 65535 of sequences exceeded in file huge.a3m

Done

In general it is possible to raise this limit if you change the constant MAXSEQ in src/hhdecl.h and rebuild/install hhsuite:

const int MAXSEQ=65535; //max number of sequences in input alignment

from hh-suite.

Can this be made an option that is passed through the command-line to hhfilter? Seems like a natural thing to do instead of having to recompile. Similarly for hhblits, etc.

from hh-suite.

It might be done, but it requires more work. At the moment, there is no developer (PostDoc, PhD or Master/Bachelor student) working on HHblits.

from hh-suite.

Are there other limits on how large MAXSEQ can get? I've tried increasing it and recompiling, but I can only get it to about 2,000,000 before hhfilter starts segfaulting on start. I'm not sure what the cause is, but I'd like to increase it a lot higher (~100,000,000) .

from hh-suite.

any update on this? i have just ran into the exact same problem myself

from hh-suite.