PBWA-samse randomly doesn't finish

[Nihil347]

Hi,

I'm using pbwa on a Computercluster (LSF-Batchsystem, so I need to load an Open MPI environment)

Homepage pbwa:

http://pbwa.sourceforge.net/

Most of the time it works flawless, but some sequences are impossibele to process with samse. In that case the sequence never gets finished and stayes in work until the respective job is killed. Output-files are not empty, so it does something.

I belive there is a correlation between the error and the number of parallel processors I set.

My cmd looks like this:

for i in SEQUNCENAME; do bsub -n 9 mpirun pBWA samse -f PATHtoSAI-files/$i -M $GENOMEPATH $i $i; done

The loop might lock a bit confusing because I call 3 times the same variable, but that is correct like this.

Any idea?

Thanks for reading!