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?