Hello !
I'm trying to blast one sequence against nt that I downloaded locally but the process hangs forever and nothing is written in the output file.
For reference, I've downloaded nt from the ncbi ftp, checked all the md5 afterwards and once everything was unzipped, I used blastdbcheck to make sure it was not corrupted.
My issue is that when trying to run the following command, it just seems to do nothing at all for a long time (I always end up killing the process after 30/40min). When I replace the nt by nt.00 for instance I do get results very quickly.
blastn -num_threads 16 -query oneseq.fasta -db nt -outfmt 7 -out test.tsv
For reference, my computer has 32Gb of ram available, but never seems to use more than 5 (rest is cache). I cannot find any "verbose" mode for blast to see if he's trying to do something or if it's really stuck and hanging somehow.
If I understood blast behavior properly, when the database is split like nt is (nt.00, nt.01 ... nt.77), blast tries to search against everything and then compile the results together. Can it be that I just don't have enough memory for assigning even a single sequence in reasonable time ? I would expect to assign at least one sequence in a few minutes.
Okay, I figured it out. I downloaded the nt database again and this time it went fine. I guess there was something wrong with the database I had. I am now a bit surprised by blastdbcheck going through just fine.