Dear all, Well, it looks like we've got Interpro running on the cluster with the Sun Grid Engine queuing system. Steps needed to make this work (technical details): 1 - Allow job submission from all nodes (!) 2 - Update qstat_ipr.pl in the iprscan/bin directory (the patch from interpro should work, basically-you need to use the -f flag for qstat). 3 - Create a symbolic link to iprscan/conf/sge6.env under iprscan/conf/sge.env 3 - Change the following line in iprscan/sge6/conf asyncsub=qsub -N [%jobid] [%optqueue] -shell n -b y -o /dev/null -e /dev/null [%env IPRSCAN_HOME]/conf/sge6-test.sh [%toolcmd] To this: asyncsub=qsub -N [%jobid] [%optqueue] -shell n -b y -o /dev/null -e /dev/null [%toolcmd] Best regards, Michael Gang Evogene Bioinformatics P.S. I would like to specially thank Mr. Powers for his great help