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