Benjamin Buchfink

Have you tried using a dmnd database instead of BLAST? BLAST databases rely on mmap which often does not work well together with certain storage types.

> I just tried using a dmnd database and it seems to work now. I did some research on FUSE and mmap, and it does seem that there may be...

Long queries can be handled better when using frameshift mode `-F 15` in combination with `--range-culling`, although the maximum I have tried were bacterial chromosomes. Some adjustments may be necessary...

That's true, it can't hurt to have a safeguard in place instead of having users find out the hard way.

I understand your concern, but I am hesitant to change the default behaviour. Many users don't take the time to properly read the manual, and could experience an unnecessary reduction...

I have to give it some more thought. Maybe there is a compromise, such as detecting the load on the system and printing a warning if necessary.

Thanks, feel free to post a pull request. `\1` used to be the character for separating different accessions. I don't know if it's still used, but backward compatibility with these...

Indeed, the behaviour of blast also depends on whether you use `-parse_seqids` and where you got the database from. Diamond databases always store the full length sequence titles, if trimming...

The repeat masking is included in the output, there is no way to prevent that at this time unfortunately. If you need the unmasked target sequence, you need to pull...

You can use `-k1` to report the best hit (in terms of evalue). Sorting by other metrics is not supported, but you can use `-k0` to report all hits and...