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Old 02-07-2017, 12:12 PM   #5
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Sounds like there's something strange about the concatenated gzipped files; it might work better if you decompress them, concatenated them, and then compress them again:

zcat left1.fastq.gz left2.fastq.gz left3.fastq.gz | gzip -c > left_all.fastq.gz
There are some versions of Java that have trouble with certain concatenated gzipped files (they think the file ends at one of the concatenation boundaries), which appears to be a bug. So you can do as above, or interleaved them with a different tool.
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