Closed prashantshingate closed 6 years ago
You can restart if you first remove the es.ovlStore.BUILDING folder. Typically on your sized genome we'd use a parallel store construction but this is disabled off grid to avoid overloading filesystems. You could add ovsMethod=forceparallel
to turn it back on since I expect your filesystem could handle the added I/O.
You're running completely off grid which slows down the compute but typically you can restart the run with the same command if it fails again.
Thank you so much for your reply. I will try ovsMethod=forceparallel option and update you about the outcome. Thank you once again for your help.
Reopen if needed.
Hello CANU team,
Thank you for creating this great assembler and the support you provide to users. I am using CANU v1.7 to assemble a genome ~1Gb in size and with ~100X PacBio raw-reads (~50X from sequel and ~50X from RSII).
I am using a supercomputer for this purpose.
There is a PBSPro scheduler, however there are lots of restrictions to submit a job. For example, memory per node is restricted to 96GB though real memory is 126GB, walltime for all jobs using (queue=normal/largemem) multiple nodes is restricted to 24 hours only while for single node job (queue=long) it is restricted to 120 hours. Also, walltime parameter is mandatory during job submission.
Due to such restrictions, I failed to start the job using Grid (it failed at 1-mercount stage itself). Hence I started a job without Grid, first on largemem queue (cores=48, memory=2TB, walltime=24:00:00) and then for ovStoreBuild stage on long queue (cores=24, memory=96GB, walltime=120:00:00).
CANU command used:
~/scratch/softwares/canu-1.7/Linux-amd64/bin/canu useGrid=false -p es -d es-pacbio2 maxMemory=96g maxThreads=24 genomeSize=1g -pacbio-raw sequel_rs2_all.fq
It worked great on the system. However, it stucked at ovlStoreBuild stage. This stage could not finish within 120 hours and when I resubmit CANU, I get following error along with last few lines of
es.ovlStore.err
.Is there any way I can configure CANU to resume from the point it stopped in ovStoreBuild stage? Sorry for long message. Thank you once again for your help and time. Best Regards, Prashant Shingate
Last few lines of correction/eshark.ovlStore.err
: