Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Samtools pileup filesize limit Mansequencer Bioinformatics 5 05-28-2013 01:08 AM
Fragment size limit Gina_P Sample Prep / Library Generation 11 01-06-2012 03:04 PM
Limit of indel length with bwa nvteja Bioinformatics 1 12-09-2010 08:46 AM
TopHat limit length maria.b Bioinformatics 2 10-21-2009 11:50 PM
maq merge limit Layla Bioinformatics 7 09-05-2009 12:58 AM

Thread Tools
Old 01-03-2012, 08:25 AM   #1
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:
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?
mscholz is offline   Reply With Quote
Old 01-03-2012, 01:08 PM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

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.
maubp is offline   Reply With Quote

bowtie2, file size limits

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:29 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO