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Old 01-03-2012, 08:25 AM   #1
mscholz
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Location: Los alamos

Join Date: May 2010
Posts: 13
Default Bowtie2 and 2 GB limit

I don't think I've posted this before.

I am attempting to do some mapping with bowtie2, and, despite any of my best efforts, I cannot get bowtie2-build to work on anything larger than 2 GB. From the announcement, it appears that the builders say that they've fixed the limitation (presumably by switching to 64 bit variables), but even when I compile with 64 bits, it still spits this error:
Quote:
Error: Reference sequence has more than 2^32-1 characters! Please divide the
reference into batches or chunks of about 3.6 billion characters or less each
and index each independently.
has anyone else had any luck?
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Old 01-03-2012, 01:08 PM   #2
maubp
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Location: Dundee, Scotland, UK

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Default

Out of interest what organism are you working on and how long are your contigs/chromosomes? I'm interested because the BAM index files (BAI) themselves currently impose quite a low limit on reference lengths - something that plant biologists at least may find a problem.
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