Message: 1 Date: Tue, 13 Sep 2011 18:32:43 +0000 From: Zachary A Lewis <zlewis@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-B5A4-0615CD80610D@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
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<zlewis@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-B5A4-0615CD80610D@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 ___________________________________________________________ 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:
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participants (2)
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Jennifer Jackson -
Pandey, Ashutosh