Message: 1
Date: Tue, 13 Sep 2011 18:32:43 +0000
From: Zachary A Lewis <>
To: "" <>
Subject: [galaxy-user] Help with sam to bam
Message-ID: <>
Content-Type: text/plain; charset="us-ascii"

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.



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. 

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