I am running the unitigging step with heterozygous options (in continuation of #848 ). The utgovl step seems to take like forever. There are 287 overlap jobs required. For each overlap job I am using 48 cores per process with 8 jobs in parallel (total cores being used 8*48). At an average I see only 2-4 jobs being completed per day.

I have the following queries:

1. Is it really expected to be this slow?
2. Is the computation resource not enough to speed this up?
3. Any way to increase the speed without compromising on the assembly quality?

Canu command:

~/apps/canu-1.7/Linux-amd64/bin/canu -assemble
 -d canu-pacbio-reutg
 -pacbio-corrected canu.trimmedReads.fasta.gz
 -p canu.utg
 gridOptions=' -N pb -l walltime=128:00:00'
 gridEngineMemoryOption='-l mem=MEMORY'
 gridEngineThreadsOption='-l nodes=1:ppn=THREADS'
 useGrid=remote
 genomeSize=1.4g
 correctedErrorRate=0.105
 "batOptions=-dg 3 -db 3 -dr 1 -ca 500 -cp 50"