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 04:57 AM
Bowtie out of memory Palgrave Bioinformatics 6 03-04-2014 07:33 PM
Bowtie: Ultrafast and memory-efficient alignment of short reads to the human genome Ben Langmead Literature Watch 2 03-04-2013 03:06 AM
bowtie memory warning crh Bioinformatics 7 08-20-2012 02:24 AM
Bowtie memory error polsum Bioinformatics 2 12-02-2011 01:17 PM

Reply
 
Thread Tools
Old 11-16-2012, 06:26 AM   #1
ChrisAU
Junior Member
 
Location: Tübingen

Join Date: Jan 2012
Posts: 9
Default bowtie chunkmbs - Exhausted best-first chunk memory

Hi,

perhaps somebody can solve this little mystery for me.

Running bowtie --chunkmbs 512 worked without any errors/warnings.
As the mapping statistic was not as I expected, among other things, I also increased the value for chunkmbs to 4096. However, on the same dataset, with the other parameters untouched, bowtie now reports "Exhausted best-first chunk memory for read..." millions of times.
At this point, the sever was using only 10% of it's overall memory.

Could somebody explain this to me please?
Chris
ChrisAU is offline   Reply With Quote
Old 02-17-2014, 12:53 PM   #2
alisrpp
Member
 
Location: New York

Join Date: Dec 2010
Posts: 40
Default

Hi ChrisAU,

Did you solve your problem? I am now having the same issue and I could use a little bit of help.

Thanks!
alisrpp is offline   Reply With Quote
Reply

Tags
bowtie, chunkmbs, memory

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 12:10 AM.


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