Hi Zach,

Would you have time to send this in as a bug report so that we can take a closer look? Format problems are likely the issue, but this can be double checked. To report as a bug, click on the green bug icon in the error dataset's box in your history. If your Galaxy account uses a different email, just note that in the comments so the two questions can be linked.


Thanks!

Jen
Galaxy team

On 9/14/11 11:01 AM, Pandey, Ashutosh wrote:


Message: 1
Date: Tue, 13 Sep 2011 18:32:43 +0000
From: Zachary A Lewis<zle...@uga.edu>
To: "galaxy-user@lists.bx.psu.edu"<galaxy-user@lists.bx.psu.edu>
Subject: [galaxy-user] Help with sam to bam
Message-ID:<ae8e036c-cbd3-46f9-b5a4-0615cd806...@uga.edu>
Content-Type: text/plain; charset="us-ascii"

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


Hi Zack,

I got a similar problem but I am not sure if you have the same problem. My problem was due to use 
of different chromosome symbol by reference fasta file and the SAM file. May be you are using 
"chr2" in SAM file and "2" in reference file or vice-versa. Converting 
chromosome symbol would be easy for reference fasta file.

Thanks
-Ash
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___________________________________________________________
The Galaxy User list should be used for the discussion of
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