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Old 06-17-2014, 03:17 AM   #8
Corydoras
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Location: Norwich

Join Date: Jan 2014
Posts: 20
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Hi Brian,

I got a file with cleaned sequence data and I want to assemble this de-novo using velvet. Due to the nature of the sequencing and the library protocol, my kmer coverage is quite variable and I wanted to use BBnorm to normalize the coverage a bit to aid the assembly. Am I correct that BBnorm is the right thing to use for this?

Anyway, currently trying to give it a go and I got this error message:

bbmap$ sh bbnorm.sh in=Fowleri_combined.fastq out=normFowleri.fastq target=15
bbnorm.sh: 104: bbnorm.sh: Bad substitution
bbnorm.sh: 112: bbnorm.sh: [[: not found
bbnorm.sh: 112: bbnorm.sh: [[: not found
bbnorm.sh: 118: bbnorm.sh: source: not found
bbnorm.sh: 119: bbnorm.sh: parseXmx: not found
bbnorm.sh: 120: bbnorm.sh: [[: not found
bbnorm.sh: 123: bbnorm.sh: freeRam: not found
java -ea -Xmxm -cp /home/martin/Downloads/bbmap/current/ jgi.KmerNormalize bits=32 in=Fowleri_combined.fastq
Invalid maximum heap size: -Xmxm
Could not create the Java virtual machine.

Any ideas?

Many thanks,

Sarah
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