rajewsky-lab / mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data
GNU General Public License v3.0
137 stars 49 forks source link

mapper.pl takes a long time for some data #110

Closed Chenmi0820 closed 1 year ago

Chenmi0820 commented 1 year ago

Hello everyone,

I have some data of samples for mapple.pl analysis. At the beginning it was smooth, with each sample taking about 10 minutes to generate the .arf file. However, for some samples which are more than 25 million but less than 30 million, it has been running for 3 days with no results but the temporary file could be generated.

Given that some samples can run properly, I think the command is fine. mapper.pl /depot/leizhang/data/name.fa -c -j -l 18 -m -p /depot/leizhang/data/meloidogyne_incognita.PRJEB8714.WBPS17.genomic -s name_collapsed.fa -t name_collapsed_vs_genome.arf

Any advice for this situation? Thanks!

Drmirdeep commented 1 year ago

Sounds like a memory issue but you will have to do some debugging. Maybe split the problematic file into half’s and run them separately

Chenmi0820 commented 1 year ago

It's actually a memory issue. Thank you!