Question: Help W Sam To Bam
0
DAR78@pitt.edu • 10 wrote:
Hi,
We're loving Galaxy. This is an excellent interface and set of tools.
The issue we're having is running SAM to BAM. We've been following
the
"Illumina Mapping: Single Reads" screencast, with the only significant
difference (I think) being that we're using our own uploaded reference
genomes instead of a pre-built index for the Bowtie alignment.
When we get to the SAM to BAM step, we have two options for "Choose
the
source for the reference list": 1. Locally Cached, 2. History.
1. If we try to use "Locally Cached", we get the following error
before
the job is even added to the queue: "Unspecified genome build, click
the
pencil icon in the history item to set the genome build". We've tried
to
follow those directions, but don't see the reference genome we want in
the
list.
2. If we try to use "History" and specify the SAM file and then the
FASTA
file we used to do the bowtie alignment, we get the following error:
An error occurred running this job: Samtools Version: 0.1.12 (r862)
Error
creating indexes from reference
(/galaxy/home/g2main/galaxy_main/database/files/001/894/dataset_189459
8.dat),
[fai_build_core] different line length in sequence
'gi|118467340|ref|NC_008596.1|'.
Segmentation fault
Any guidance would be wonderful.
My user name is: dar78@pitt.edu
Thanks for your help,
Dan Russell
University of Pittsburgh
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modified 7.9 years ago
by
Kelly Vincent • 340
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written
7.9 years ago by
DAR78@pitt.edu • 10
