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Old 02-12-2019, 11:40 AM   #8
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,881

I am wondering if the error you are seeing is a red herring. How much memory are you allocating to this job on the cluster (bbsplit can need a lot of memory depending on size of the reference genomes).

You should explicitly add "-Xmx20g" (this is 20 gig, just an example) flag to your bbsplit command. Make sure you match the sample amount of memory on the cluster side.

On a side note:

validateFiles -type=fastq QualTrimmed_bran11.fasta
generated an error since you need to change the type to fasta to match. So try

validateFiles -type=fasta QualTrimmed_bran11.fasta
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