Hello Mary,
The underlying data is not complete for all mm9 reference genomes for
the Bowtie2/Tophat2 tools, causing the error. It is a known issue and we
expect to have it corrected very soon now. We consider this important
and high priority, our apologies for the confusion it caused.
A list of known data issues since the migration of usegalaxy.org are
listed in this ticket. You can follow the ticket to find out when this
genome has been restored: https://trello.com/c/SbizUDQt
Best,
Jen
Galaxy team
On 10/29/13 7:43 AM, Davis, Mary wrote:
Greetings---
I tried to run an alignment using Bowtie2 and got this message-
format: bam, database: mm9
Could not locate a Bowtie index corresponding to basename
"/galaxy/data/mm9/mm9canon/bowtie2_index/mm9canon" Error: Encountered
internal Bowtie 2 exception (#1) Command:
/galaxy/software/linux2.6-x86_64/pkg/bowtie2-2.1.0/bin/bowtie2-align
--wrapper basic
I imported Illumina fastq data, groomed them, and then did the
analysis using the built-in index mouse, both full and male, and had
the same error message.
I'm relatively new to this, and don't see what I missed.
Thanks
Mary E. Davis, Ph.D.
Professor
Department of Physiology & Pharmacology
West Virginia University Health Sciences Center
PO Box 9229
Morgantown, WV 26506-9229
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--
Jennifer Hillman-Jackson
http://galaxyproject.org
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