Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Is bowtie2 really this unstable? kgulukota Bioinformatics 5 02-22-2012 09:27 AM
Bowtie2 --al and --un: no output arnav Bioinformatics 3 02-14-2012 02:08 PM
Bowtie2 ( not running with option --sam-rg CHRYSES Bioinformatics 2 01-24-2012 03:28 AM
Bowtie2 with Tophat plassaaw Bioinformatics 4 11-11-2011 07:12 AM
tophat Error running running 'prep_reads' victoryhe Bioinformatics 2 10-17-2011 05:53 AM

Thread Tools
Old 01-16-2012, 02:47 AM   #1
Junior Member
Location: germany

Join Date: Oct 2010
Posts: 2
Default Bowtie2 running infinitely


I am using Bowtie2.0.0-beta4 to map Illumina raw reads to a file with a lot of fasta sequences in it.

I have Illumina GAIIx data (75b reads, single end file size is 9 GB) and HiSeq data (100b reads, single end file size is 12 GB or 20GB).

When mapping with these options:
bowtie2 -x repbase_nov11_TEs/ref_fasta.indexed -q -U ../../singleend_rawreads.fastq --sensitive-local -a -p 6 -S mapped.sam

everything works fine for the GAIIx data and the HiSeq data when I use a fasta ref with 5 sequences in it.

But if I use a bigger fasta ref (60 megabytes), then it works fine for GAIIx, but with HiSeq data it seems to run infinitely on.
When I look at the size of the generated sam file, it increases two a not specific size and then it stops increasing the file size, but the processors are still working (though of the 6 started, sometimes only 4 go on after this size was reached).

I thought probably the fasta-ref or the raw data input size is too big . For both I used only a fraction, but the same problem occurs again.

This is strange, because the exact same data with another fasta-ref (the small one) worked just fine.

Also, I run it on another system with 48 cores and there, the *.sam file increases to 50GB and then stops increasing, but CPUs keep running. If I start it with 6 cores, then it gets just to about ~10GB.

And I waited like 5 days... so I do not think it will stop.

I like bowtie2 really much, and it is doing exactly like i wanted my stuff, so I will be grateful if someone could give me a hint how to solve this problem.

Best wishes,
jaZt is offline   Reply With Quote

bowtie2, mapping, running infinitely

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 02:40 PM.

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