Open ajkarloss opened 12 months ago
Background: MLST takes 2+ hours to run. It supposed to take about 20 mins.
We mention "--threads 16 --memory 32" for Shovil to be used by Spades.
Commad used ''' spades.py --pe1-1 flash.notCombined_1.fastq.gz --pe1-2 flash.notCombined_2.fastq.gz --only-assembler --threads 8 --memory 4 -o spades --tmp-dir /opt/galaxy/tmp -k 31,55,79,103,127 --threads 16 --memory 32 --tmp-dir /opt/galaxy/tmp/ --pe1-m flash.extendedFrags.fastq.gz 2>&1 | sed 's/^/[spades] /' | tee -a shovill.log '''
But it looks like its running on just 1 node and 8CPU.
ajkarloss
commented
12 months ago ajkarloss
commented
12 months ago
Background: MLST takes 2+ hours to run. It supposed to take about 20 mins.
We mention "--threads 16 --memory 32" for Shovil to be used by Spades.
Commad used ''' spades.py --pe1-1 flash.notCombined_1.fastq.gz --pe1-2 flash.notCombined_2.fastq.gz --only-assembler --threads 8 --memory 4 -o spades --tmp-dir /opt/galaxy/tmp -k 31,55,79,103,127 --threads 16 --memory 32 --tmp-dir /opt/galaxy/tmp/ --pe1-m flash.extendedFrags.fastq.gz 2>&1 | sed 's/^/[spades] /' | tee -a shovill.log '''
But it looks like its running on just 1 node and 8CPU.