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Old 06-30-2016, 09:15 AM   #41
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Originally Posted by gringer View Post
From the error messages, your input read files are corrupted:

Do you have any other program that can read the files to check for errors? At the very least, a simple count of lines would be useful:

wc -l read1.corrected.fq.gz; wc -l read2.corrected.fq.gz
[numbers should be identical, and this should produce no errors]
Gringer is correct; the files appear to be corrupt. But just to add a small correction, it does not look like wc can handle gzipped files, so I'd suggest either:

zcat read1.corrected.fq.gz | wc -l; zcat read2.corrected.fq.gz | wc -l
...which I have no idea how it would behave on a corrupt file, but should produce a correct answer for a correct file. Or this:
gzip -t read1.corrected.fq.gz; gzip -t read2.corrected.fq.gz
...which will test the integrity of the files. It seems to print nothing if the file is OK; if the file is truncated, it will print:
gzip: x.gz: unexpected end of file
Probably, the process generating the corrected files (probably Tadpole) was killed or timed out before it was finished.
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