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Old 02-07-2019, 04:46 AM   #321
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,992
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We are making progress!

How much memory do you have on this Mac? I suggest using 85% of the maximum memory you have available with BBTools. You also need to specify "in1= and out1=" to go with in2= out2= etc. Since you are using IUPAC bases in your literal sequence you also need to run this option on

copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all
possible unambiguous copies.

You are also trimming to the left side of the read. Is that correct?

Can you try this command?

Code:
bbduk.sh -Xmx4g in1=sample14_S14_R1.fastq.gz in2=sample14_S14_R2.fastq.gz out1=sample14_S14_R1_btrimmed.fastq.gz out2=sample14_S14_R1_btrimmed.fastq.gz literal=GTACACAMCGCCCGTCGC,TGATCCTTCTGCVGGTTCWCCTACG k=10 ordered=t mink=2 ktrim=l rcomp=f minlength=50 maxlength=155 copyundefined=t tbo tpe
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