I'm running a small assembly. The command options are:
-pacbio-raw reads.fasta genomeSize=60000 -d assembly -p asm useGrid=false gnuplotTested=true corMhapSensitivity=high corMinCoverage=1 cnsThreads=4 ovlThreads=4 mhapThreads=4 contigFilter="2 1000 1.0 1.0 2"
During the trimming phase (command below), it stalls on the gnuplot command. Checking for running jobs shows:
sh -c gnuplot ./asm.1.trimReads.inputReads.gp > /dev/null 2>&1
When I go to the assembly directory and run the command without redirection:sh -c gnuplot ./asm.1.trimReads.inputReads.gp, it enters the gnuplot shell.
If I instead run:sh -c gnuplot < ./asm.1.trimReads.inputReads.gp it ends without problems.
I'm trying to track down the source of this since I've been able to run canu commands before, so it's possibly something changed on our cluster. However, if it is possible to add an option to skip plotting, this will reduce some file IO and this issue.
The trimming step:
cd trimming/3-overlapbasedtrimming
/auto/cmb-16/mjc/shared/software_packages/canu/Linux-amd64/bin/trimReads \
-G ../asm.gkpStore \
-O ../asm.ovlStore \
-Co ./asm.1.trimReads.clear \
-e 0.045 \
-minlength 1000 \
-ol 1 \
-oc 1 \
-o ./asm.1.trimReads \
> ./asm.1.trimReads.err 2>&1
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