Milot Mirdita

I think this error can happen if there is a space (or possible other whitespace) after the `>` and before the accession.

Then I am quite confused :D Would it be possible to share the FASTA file that causes this error? If not, can you try to "bisect" the file and try...

Do you happen to know in which of these FASTA files the error occurs? That would help me reproduce the issue.

You could do a kind of binary search, just take half of the FASTA files each time. It should take at most 9 `createdb` calls to figure it out. However,...

Are you writing to a fast storage system? I assume it is IO limited and not compute-limited.

Is this with the latest release? We had a few changes a while ago that are only officially part as of release 15 Maybe the issue is already fixed. I...

You can disable the E-value threshold `-e inf`. However, this doesn't sounds like a biologically meaningful task, as it might return non-homologous sequences.

There are a few accession formats (uniprot, gi, ...) that use pipes and we parse out the meaningful part of the accession. You can override the default output format to...

No, currently query/target always parses the accession: ``` { "uc", 2, 0}, // Uniclust { "cl|", 3, 1}, { "sp|", 3, 1}, // Swiss prot { "tr|", 3, 1}, //...

This is a bit of a common footgun with MMseqs2: https://github.com/soedinglab/MMseqs2/wiki#how-does-mmseqs2-compute-the-sequence-identity MMseqs2 by default only determines accurate bit-scores and E-values and does not compute the full alignment, instead of just...