Question: Help With Sam To Bam (Zachary A Lewis)
gravatar for Pandey, Ashutosh
7.2 years ago by
Pandey, Ashutosh10 wrote:
Message: 1 Date: Tue, 13 Sep 2011 18:32:43 +0000 To: "" <> Subject: [galaxy-user] Help with sam to bam Message-ID: <> 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
alignment bowtie samtools bam • 1.1k views
ADD COMMENTlink modified 7.2 years ago by Jennifer Hillman Jackson25k • written 7.2 years ago by Pandey, Ashutosh10
gravatar for Jennifer Hillman Jackson
7.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson
ADD COMMENTlink written 7.2 years ago by Jennifer Hillman Jackson25k
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