Hi all,

I downloaded and installed Segemehl aligner and created an index file which completed as expected. I am trying to align a 150 GB fastq file to grch38.p2 and when i run the following command I can see segmhel as one of the processes. However the process does not seem to use multithread, the server has 16 cores and after setting 8 thread usage it still uses only one thread. The OS is Ubuntu 14 LTS.

http://www.bioinf.uni-leipzig.de/Software/segemehl/

./segemehl.x -i genome.idx -d genome.fa -q data.fa --threads 8 > alignment.sam

Has anyone else also faced the same problem? Anything I am missing here?

Thanks in advance.