cat make_msa.stderr

[Niohuruzh]

Hello everyone, I have a question about the file after cat make_msa.stderr WARNING: Maximum number 65535 of sequences exceeded in file /home/../hhblists/tooo_.1e-30.a3m

If you have the same question, could you tell me how to fix it? Thanks!!!

[1000000000000000000000000000000]

I have also been experiencing this warning.

[Niohuruzh]

I have also been experiencing this warning. So did you produce the t000_e2e.pdbfile?

[pguillem]

The 65535 number sounds suspiciously tied to a 16 bit integer (or array index) that should be way bigger. Perhaps the number of sequences was never ment to be that high?.

Reading on HHblits, it seems variable MAXSEQ in the sourcecode controls the max amount of sequences in a file. People also report that they managed to increase this value to nearly 2 million, before starting to get segfaults.

Read https://github.com/soedinglab/hh-suite/issues/51

They reported adding the option -maxseq to tackle the issue. I imagine you can download the HHblits source, modify this variable, and compile it yourself. Or include the parameter -maxseq 512000 (or something alike) in the cmd.