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
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
