I'm confused how to convert my current canu command to mecat2canu. I have several parameters that are specific for my cluster. Both mecat2canu options have grid=0. Can I set grid=1 and pass all of the parameters below?
module load jdk/1/8;
/fslgroup/cotton_seq/compute/software/canu-1.7.1/Linux-amd64/bin/canu -d canu5 -p Lupin genomeSize=900m corMhapSensitivity=normal minReadLength=2000 minOverlapLength=800 merylMemory=240g merylThreads=16 ovsMethod=parallel gridOptions="--time=2:00:00 --mem-per-cpu=10g" gridOptionsOVS="--mem-per-cpu=10g --time=24:00:00" gridOptionsExecutive="--time=12:00:00" gridOptionsCORMHAP="--mem-per-cpu=32g --time=2:00:00" gridOptionsOBTMHAP="--mem-per-cpu=10g --time=2:00:00" gridOptionsUTGMHAP="--mem-per-cpu=10g --time=2:00:00" gridOptionsCOROVL="--mem-per-cpu=12g --time=48:00:00" gridOptionsOBTOVL="--mem-per-cpu=12g --time=48:00:00" gridOptionsUTGOVL="--mem-per-cpu=12g --time=48:00:00" gridOptionsRED="--mem-per-cpu=10g --time=2:00:00" gridOptionsOEA="--mem-per-cpu=12g --time=48:00:00" -pacbio-raw cat reads_fastq.lst
I'm confused how to convert my current canu command to mecat2canu. I have several parameters that are specific for my cluster. Both mecat2canu options have grid=0. Can I set grid=1 and pass all of the parameters below?
module load jdk/1/8;
/fslgroup/cotton_seq/compute/software/canu-1.7.1/Linux-amd64/bin/canu -d canu5 -p Lupin genomeSize=900m corMhapSensitivity=normal minReadLength=2000 minOverlapLength=800 merylMemory=240g merylThreads=16 ovsMethod=parallel gridOptions="--time=2:00:00 --mem-per-cpu=10g" gridOptionsOVS="--mem-per-cpu=10g --time=24:00:00" gridOptionsExecutive="--time=12:00:00" gridOptionsCORMHAP="--mem-per-cpu=32g --time=2:00:00" gridOptionsOBTMHAP="--mem-per-cpu=10g --time=2:00:00" gridOptionsUTGMHAP="--mem-per-cpu=10g --time=2:00:00" gridOptionsCOROVL="--mem-per-cpu=12g --time=48:00:00" gridOptionsOBTOVL="--mem-per-cpu=12g --time=48:00:00" gridOptionsUTGOVL="--mem-per-cpu=12g --time=48:00:00" gridOptionsRED="--mem-per-cpu=10g --time=2:00:00" gridOptionsOEA="--mem-per-cpu=12g --time=48:00:00" -pacbio-raw
cat reads_fastq.lst