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Old 06-17-2014, 10:14 AM   #9
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,695


Yes, BBNorm is the correct tool.

I'm not sure, but I suspect that your shell is not bash. You could retry the command with "bash" instead of "sh", which may work. But the easier thing is just to skip the shellscript and invoke java manually:

java -ea -Xmx14g -cp /home/martin/Downloads/bbmap/current/ jgi.KmerNormalize bits=32 in=Fowleri_combined.fastq out=normFowleri.fastq target=15

That command would work if you had 16g of RAM. Just set the -Xmx parameter (highlighted in purple) to about 85% of however much RAM is on the machine. If you don't know, you should be able to find out like this on a Linux system:

cat /proc/meminfo

...then look at the first line, "MemTotal".

However, 15x is a fairly low target depth. For velvet I would suggest at least 30x for an optimal assembly, unless you just don't have enough data.

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