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Old 06-22-2014, 09:31 PM   #15
woodydon
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Location: https://www.researchgate.net/profile/Woody_Lin

Join Date: Jan 2010
Posts: 52
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Hi Brain,

I am using a computing cluster to run BBMerge and found the following error:

Quote:
java -ea -Xmx48g -cp /home/xxx/tools/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 -Xmx48g in1=/home/xxx/reads/n_R1.fastq in2=/home/xxx/reads/n_R2.fastq ref=/home/xxx/ref/hg19c/genome_hg19.fa ihist=/home/xxx/bbmap/n_ihist.txt out=/home/xxx/bbmap/n_merged.fq
/home/xxx/tools/bbmap/bbmap.sh: line 176: java: command not found
my command was:
Quote:
/home/xxx/tools/bbmap/bbmap.sh -Xmx48g threads=10 in1=/home/xxx/reads/n_R1.fastq in2=/home/xxx/reads/n_R2.fastq ref=/home/xxx/ref/hg19c/genome_hg19.fa ihist=/home/xxx/bbmap/n_ihist.txt out=/home/xxx/bbmap/n_merged.fq

Thanks,
Woody

Last edited by woodydon; 06-22-2014 at 09:36 PM.
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