When I run blastn -numthreads 6 -task blastn-short -db humangenomic on one 36 bp query it typically takes less than a minute and occupies up to about 5GB. When I gave it a file (using -query) of 606 queries all of the same length, blast took all weekend (8.5 mins each on average). Top suggests it was trying to use 60 gigabytes of memory. Also time says instead of running six times faster (-num_threads 6) it was only effectively using 27% of one CPU.
Is this expected? My plan is in future to split the query file into 6 and run then in series. Does that sound sensible?
(the server has 8 CPUs and 32 MBytes)
Many thanks Bill
ps: the font in this window is too small for me:-(
Update: I tried spliting another file queries into ten files each of either 56 or 57 queries each. Even the slowest of these averaged about three queries per minute. Whilst the fasted did more than 12 per minute.