mapper.pl takes a long time for some data

[Chenmi0820]

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]

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]

It's actually a memory issue. Thank you!