Thanks Austin, good suggestions all around. The question came through
again, so I didn't realize this was completely solved. Glad this was
just a format issue!
Take care,
Jen
Galaxy team
On 9/14/11 4:54 PM, Austin Paul wrote:
Hi Zach,
You should reply to all so people dont keep working on your questions.
Glad to help.
Austin
---------- Forwarded message ----------
From: *Zachary A Lewis* <zle...@uga.edu <mailto:zle...@uga.edu>>
Date: Tue, Sep 13, 2011 at 3:10 PM
Subject: Re: [galaxy-user] Help with sam to bam
To: Austin Paul <austi...@usc.edu <mailto:austi...@usc.edu>>
Thanks Austin! That did the trick.
Zack
On Sep 13, 2011, at 4:47 PM, Austin Paul wrote:
You could try "fasta width formatter" on your reference fasta. This
has helped me in the past when I received a similar error.
On Tue, Sep 13, 2011 at 11:32 AM, Zachary A Lewis <zle...@uga.edu
<mailto:zle...@uga.edu>> wrote:
Hi,
I was wondering if someone could help me with an error message I'm
getting after performing a sam to bam conversion in galaxy. I've
used Bowtie to map sequence reads to a custom fasta file
corresponding to one chromosome in my organism. The mapping seems
to work fine, but when I attempt a sam to bam conversion, I
receive the folowing error message:
An error occurred running this job: /Samtools Version: 0.1.12 (r862)/
/Error creating indexes from reference
(/galaxy/main_database/files/002/977/dataset_2977193.dat),
[fai_build_core] line length exceeds 65535 in sequence 'LGVII'.
Segmentation fault/
/
/
Any help would be appreciated.
Thanks,
Zack
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