Martin Steinegger

This sounds like a filesystem error while closing the result file. Could it be possible that the system ran out of space?

Here you can read more about MMseqs2: https://github.com/soedinglab/MMseqs2/wiki

Thank you for reporting this. I see whats happening here. The prefilter sets the k-mer threshold to 130. None of the k-mers in the sequence reaches that threshold. So no...

You can use the `--format-output` parameter to define your custom columns in the output format. Read more about this [here](https://github.com/soedinglab/mmseqs2/wiki#custom-alignment-format-with-convertalis).

The maximal size for one clustering can not be more than (2^32 - 1), which is roughly 4 billion sequences. To cluster 16 billion you need some kind of step...

MMseqs2 is optimized to process multiple queries at once. So it would make sense to package your search into a big fasta file. If you'd like to perform fast single...

@juliacpowell1999 Yes you can get the target sequences by adding `tseq` to the `--format-output` options. For example: ``` easy-search query target result tmp --format-output query,target,tseq ```

``` awk '{print ">"$2; print $3}' result > result.fasta ```

The cluster order can be different in the output file. However the cluster itself should have the same members. Are the members changing or just the cluster order?

No, we do not filter for orthology in our clustering. They are homologous.