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Old 04-16-2012, 12:17 PM   #4
cwisch88
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Location: St. Louis

Join Date: Jan 2012
Posts: 15
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Okay well let me get the full story here.

What does the command "go" do? Are these reads that you suspect to be the problem?

From what I can tell, when this happens to me I get a number like 1310720 ok X.XX sec. and then I receive the segmentation fault.

So far I have deduced that the number represents how many read pairs that it has processed before failing.

Now, it only reports that the alignments are okay for each batch of 131072, so if I take out that block of reads, it continues until it hit something else!

I'm thinking it might be a q-score problem, but I'm having trouble wrapping my mind around the standards:

FASTQ formats
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