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...<br>
<br>Best,<br>Dan<br><br><div class="gmail_quote">On Tue, Apr 6, 2010 at 1:20 PM, Weng Khong Lim <span dir="ltr">&lt;<a href="mailto:wengkhong@gmail.com">wengkhong@gmail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi all,<div><br></div><div>I&#39;m new to next-gen sequencing, so please be gentle. I&#39;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:</div>

<div><br></div><div><span style="font-family: &#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif; font-size: 12px; color: rgb(48, 48, 48); line-height: 14px;">An error occurred running this job: <i>Error aligning sequence. requested number of bytes is more than a Python string can hold</i></span></div>

<div><font color="#303030" face="&#39;Lucida Grande&#39;, verdana, arial, helvetica, sans-serif" size="3"><span style="font-size: 12px; line-height: 14px;"><i><br></i></span></font></div>
<div><font color="#303030" face="&#39;Lucida Grande&#39;, verdana, arial, helvetica, sans-serif" size="3"><span style="font-size: 12px; line-height: 14px;">Can someone help point out my mistake? My history is accessible at <a href="http://main.g2.bx.psu.edu/u/wengkhong_lim/h/chip-seq-pilot-batch" target="_blank">http://main.g2.bx.psu.edu/u/wengkhong_lim/h/chip-seq-pilot-batch</a></span></font></div>

<div><font color="#303030" face="&#39;Lucida Grande&#39;, verdana, arial, helvetica, sans-serif" size="3"><span style="font-size: 12px; line-height: 14px;"><br></span></font></div>
<div><font color="#303030" face="&#39;Lucida Grande&#39;, verdana, arial, helvetica, sans-serif" size="3"><span style="font-size: 12px; line-height: 14px;">Appreciate the help!</span></font></div>
<div><font color="#303030" face="&#39;Lucida Grande&#39;, verdana, arial, helvetica, sans-serif" size="3"><span style="font-size: 12px; line-height: 14px;"><br></span></font></div><font color="#888888">
<div><font color="#303030" face="&#39;Lucida Grande&#39;, verdana, arial, helvetica, sans-serif" size="3"><span style="font-size: 12px; line-height: 14px;">Weng Khong, LIM</span></font></div>
<div><font color="#303030" face="&#39;Lucida Grande&#39;, verdana, arial, helvetica, sans-serif" size="3"><span style="font-size: 12px; line-height: 14px;">Department of Genetics<br>
University of Cambridge<br>E-mail: <a href="mailto:wkl24@cam.ac.uk" target="_blank">wkl24@cam.ac.uk</a> <br>Tel: +447503225832</span></font></div>
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<br></blockquote></div><br><br clear="all"><br>-- <br>Dan Webster<br>Ph.D. Student - Cancer Biology<br>Laboratory of Paul Khavari<br>CCSR BLDG, Rm 2150<br>269 Campus Drive<br>Stanford, CA 94305<br><a href="mailto:DanWebster@stanford.edu">DanWebster@stanford.edu</a><br>