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Old 08-19-2014, 07:55 AM   #1
ruggedtextile
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Location: Cambridge

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Default bcl2fastq 2.0 barcode mismatch option

I'm trying to run bcl2fastq with the barcode-mismatch option set to 3. Unfortunately setting this option to anything other than the default seems to result in runaway memory usage (fills and eventually kills a 128GB machine). Is this a known bug? The version I am using is:

BCL to FASTQ file converter
bcl2fastq v02.14.01.07
Copyright (c) 2007-2013 Illumina, Inc.
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Old 09-08-2014, 01:56 PM   #2
IsmailM
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BCL to FASTQ file converter
bcl2fastq v02.14.01.07
Copyright (c) 2007-2013 Illumina, Inc.

This version has so many bugs in it. You should just upgrade to their new version 2.15. Also, which is kind of lame of illumina, but they will not support version 2.14.

3 mismatches? That's a lot of mismatches in at most a 8 barcode sequence.
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Old 09-09-2014, 12:32 AM   #3
ruggedtextile
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Yes, I upgraded. 2.14 was a car crash bug-wise.

Re: 3 mismatches - yes the experiment was a bit of a car crash as well (over clustered), just trying to see what we can salvage.
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