There is a bug in Bowtie right now. We have the fix for this ready, but it won't be available until the main server is updated and restarted. In the meantime, you can use Bowtie on our test server (http://test.g2.bx.psu.edu/), which has the updated code on it (just be aware that you can't transfer history items directly from our test server to main). I am sorry for the inconvenience.


On 4/6/10 4:33 PM, Dan Webster wrote:
I have had the same problem, and am also a newbie to NGS with Illumina.  The work-around I found was to download bowtie directly from the website, run it on your local computer, then upload the resulting SAM file for subsequent Galaxy-driven analysis.  Not optimal, I know, but if you are in a hurry...


On Tue, Apr 6, 2010 at 1:20 PM, Weng Khong Lim <wengkhong@gmail.com> wrote:
Hi all,

I'm new to next-gen sequencing, so please be gentle. I've just received a pair of Illumina FASTQ files from the sequencing facility and intend to map them to the hg19 reference genome. I first used the FASTQ Groomer utility to convert the reads into Sanger reads. However, when running Bowtie for Illumina on the resulting dataset under default settings, I received the following error:

An error occurred running this job: Error aligning sequence. requested number of bytes is more than a Python string can hold

Can someone help point out my mistake? My history is accessible at http://main.g2.bx.psu.edu/u/wengkhong_lim/h/chip-seq-pilot-batch

Appreciate the help!

Weng Khong, LIM
Department of Genetics
University of Cambridge
E-mail: wkl24@cam.ac.uk 
Tel: +447503225832

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Dan Webster
Ph.D. Student - Cancer Biology
Laboratory of Paul Khavari
CCSR BLDG, Rm 2150
269 Campus Drive
Stanford, CA 94305
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