gsMapper issues

[mjleaks]

I'm having some difficulties with a gsMapper run. Hoping someone might be able to help. It seems to be very slow (it's throwing the "stalled" error message but continues to run based on what I see with "top"). Has been running over the weekend. I know that there can be issues with the software either truly hanging or simply apparently hanging when carrying out a large assembly or mapping or one with more than average repetitiveness, but I'm a bit suspicious in this instance because this run has only 100 reads. I am mapping versus the human genome in addition to a compilation of short bacterial sequences, so the reference sequence set is large, but the number of reads is so small.... Any thoughts anyone has on this would be most welcome. Thanks for having such an excellent forum

[gaster]

This sounds like it has taking too long. I don't know about your specific assembly, but my experience running Mapper off our server and assembling small <1mb genomes is that is very fast-- less than 15 minutes. I think I have seen in some other threads here that it can take much longer, but that long???. I would dig around a bit.

Are you using more than one reference sequence? Not sure how that would work. Maybe try it with just your smallest reference sequence just to make sure it is working correctly.

Dunno if that helps but at least you have my solidarity and commiseration.

Good luck!