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 <zlewis@uga.edu>
Date: Tue, Sep 13, 2011 at 3:10 PM
Subject: Re: [galaxy-user] Help with sam to bam
To: Austin Paul <austinpa@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 <zlewis@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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