I'm trying to predict targets for miRNA sequences, and so far after reading some papers for other tools that do this, I've found that I should be using FASTA's ssearch36 for this.

I'm starting with a small file of 500 miRNA sequences, searching a reference DB of 50k sequences. When using ssearch, I get the following output at the very bottom after ~85 minutes of running:

Total Scan time: 294.000 Total Display time: 4681.000

I am piping the output to a file, and the result file is ~13 Gb. It is taking this long even when I pipe the output to >nul so I don't think it's my disk speed.

I'm wondering if there's any way to speed this up, since it seems very unreasonable to me that the actual search itself only takes ~5 minutes but yet taking over an hour to simply generate output. Is it a bug or am I interpreting it incorrectly?

  • $\begingroup$ are you using the parallel or MPI version? If so, you can add more threads with the -T option. However, this probably won't help since the default is to use as many processors as are available $\endgroup$ May 11 '21 at 6:07

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