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Old 06-25-2014, 12:52 AM   #3
TonyBrooks
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Location: London

Join Date: Jun 2009
Posts: 298
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I've spoken to Illumina tech support and they have pointed out a possible bug in bcl2fastq v2.

"We identified a bug caused by thread handling that in certain cases caused errors in the order of reads such that R1 and R2 files were not in the same order. This is intermittent and may fit with your experience since it depends purely on the thread memory handling which can differ from run to run."

I've re-created the fastq using a single thread. It obviously takes 8 times as long, but I'm not seeing the picard error this time. They've promised a new version with the bug fixed any day now, so keep your eyes open.
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