Benjamin Buchfink
Benjamin Buchfink
This should be fixed in the latest release.
A profile feature is planned but will not be available in the near future.
Sequences this long will only work efficiently in frameshift alignment mode, so you should set `-F 15 --range-culling`. Also there's a known performance issue with this in the current version,...
Ok, let me know if you still need any help.
There are various other things that can prevent short alignments from being reported, including the evalue (-e), hamming distance filter (--id2), ungapped filter (--ungapped-evalue-short and --ungapped-evalue), gapped filter (--gapped-filter-evalue).
> from the wiki "Note that these two modes [sensitive and ultra-sensitive] benefit only slightly from increasing this parameter". is this ok? Seems ok, you will not get a big...
There is a known issue that is potentially causing this. It will be fixed in the next release. To access this patch now, you can clone the repository and compile...
Please try again with the latest commit.
`--iterate` will run multiple search rounds with increasing sensitivity. It will usually find the best hit for the query, but it will stop looking once a hit has been found....
For writing the output a table containing all accessions of the input sequences needs to be loaded into memory. Looks like this is causing the OOM. I can provide a...