MagicBLAST only using one thread

Question

[daewowo]

I am using the -num_threads option for magicBLAST and running from a linux shell. However only one thread is used (tried on 2 machines). The file.fa is only 20MB.

magicblast -query file.fa -db nt -num_threads 16 -out out.sam -no_unaligned

Any ideas?

[Arsenal]

No big deal of a help, but, previously I had some similar issues with other tools and the problem was dependencies needed to do parallel processing.

[daewowo]

I have no issue with multithreading using other apps eg bwa, bowtie2 etc use mutithreads OK. Wondering if if could be due to the large size of the nt database (120GB)

[Arsenal]

Ok. Then you can just test using a smaller db, and tell us if it worked

Answer 1

[daewowo]

After 20 min was using multiple threads. I presume there is a stage when magicBLAST only uses a single thread when starting. NB I also reduced num_theads to 4 but havent tested if that has anything to do with it (24 thread machine)