Benjamin Buchfink
Benjamin Buchfink
Not sure since I tested it with the same file and it worked fine. Please double check that you have cloned the latest version of the repo, compiled from source...
How big are your assemblies and how many threads do you run?
How long is the longest contig?
The longest I tested were bacterial chromosomes, but queries of >700 MB can easily break the current code. I do plan to rework the blastx mode which will probably happen...
You could try that too but I assume that the length is the problem. May I also ask why extracting ORFs is not an option for you? Are you looking...
I would guess subprocess.run will insert additional quotation marks around `6 qseqid sseqid pident length evalue bitscore full_sseq`. Not sure how to best work around that. If needed I can...
I added a message like that: 810b6834a4a807cfa053112cfbd3d6979a0af43c: I think you probably need to do this: `'6', 'qseqid', 'sseqid', 'pident'` etc.
Hi Oliver, this could very well improve the runtime in such cases and would not be too difficult to implement. However, if you do a lot of these small query...
Ok, it should be possible to include this in a future release. Note that it may also help to use a BLAST database, as it takes advantage of memory mapping....
Sorry I didn't find the time yet to work on this. But thanks for reminding me, I'll see what I can do.