I have the set of yeast genomes (136 genomes, ~9Mb and 6000 sequences each) and would like to find group of orthologous genes in them using OMA standalone.
Due to the size of data-set I am trying to arrange the parallelization of OMA run using the cluster with SGE scheduler.
First, I run
oma -c to convert the databases.
Then I submitted the jobs using command
qsub -t 1-32 -cwd run_oma.sh
the run_oma.sh contains two lines:
export NR_PROCESSES=32 oma
Then I see that all jobs are running, however, I see very big estimated remaining times which haven't decreased within 6 hours (~ 150000 h). So I am not sure that the run is parallelized properly.
Can anyone help to find out what is happening and how can I speed up the calculation?
Kind regards Marina