John Martin

Just wanted to report back that LSF works fine for PBSuite, my problem was just some bad syntax

And actually, if it doesn't support LSF could I manually run all the shell scripts in such a way that PBJelly could pick up and continue on with the steps after mapping?

I'm trying to submit the mapping portion of pbjelly to an LSF cluster (using 'bsub'). I've split the subreads fastq into 200 parts and I had thought I setup the Protocols.xml file correctly. But when I run Jelly.py mapping Protocol.xml it builds all the shell scripts but doesn't launch anything. Does PBJelly support LSF/bsub? Here is how I setup my cluster command: <cluster> echo '${CMD}' | bsub -N "${JOBNAME}" -o ${STDOUT} -e ${STDERR} -n 200 -M 31000000 -R 'rusage[mem=30000]' -a 'docker(jmartin7/ubuntu:pbsuite)'...