SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bowtie, an ultrafast, memory-efficient, open source short read aligner Ben Langmead Bioinformatics 514 03-13-2020 03:57 AM
Error with Cufflinks, ran out of memory ykingh RNA Sequencing 2 12-08-2012 05:56 PM
bowtie memory warning crh Bioinformatics 7 08-20-2012 01:24 AM
cufflinks memory allocation error. billthebrute RNA Sequencing 3 10-06-2011 06:00 AM
BFAST memory error in postprocess Marisa_Miller Bioinformatics 3 09-18-2010 04:35 AM

Reply
 
Thread Tools
Old 12-01-2011, 02:29 PM   #1
polsum
Member
 
Location: Texas

Join Date: May 2009
Posts: 32
Default Bowtie memory error

Hi - I am getting following error with bowtie

"Error: Could not allocate ChunkPool of 67108864 bytes
terminate called after throwing an instance of 'int'"

Our computer has 12 GB memory with quadcore processor. The fasta file size is about 470MB and I am mapping it to the mouse genome. I am using Ubuntu 11.10 OS.

I am using following options: -f --best --quiet -m10 -v2 --fullref --un --al --max -p32 -S m_musculus_ncbi37

Has any one encountered similar problem?

THanks in advance for any help.

Last edited by polsum; 12-01-2011 at 02:31 PM.
polsum is offline   Reply With Quote
Old 12-02-2011, 12:55 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Perhaps there are some strict memory limits being enforced; check "ulimit -a".
dpryan is offline   Reply With Quote
Old 12-02-2011, 12:17 PM   #3
polsum
Member
 
Location: Texas

Join Date: May 2009
Posts: 32
Default

Ok I was using 32-bit OS and I removed it and installed 64-Bit OS and its working without any problems. Apparently 32-bit version cant use more than 4GB memory.
polsum is offline   Reply With Quote
Reply

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 12:27 AM.


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