You could try "fasta width formatter" on your reference fasta.  This has
helped me in the past when I received a similar error.

On Tue, Sep 13, 2011 at 11:32 AM, Zachary A Lewis <zle...@uga.edu> wrote:

>  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
>
>
>
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