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Old 10-13-2014, 08:38 AM   #6
Brian Bushnell
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Location: Walnut Creek, CA

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This was caused by the bases and qualities having different lengths. Either the fna and qual file do not go together, or their order is different, or one of the files is misformatted.

"reads.fna" should already be in fasta format, though, which is what you specified as the output format. If you want fastq, the output filename needs to end with "fastq".

I suggest you post the first sequence in the reads.fna and reads.qual so we can see what's going on.
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