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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___________________________________________________________
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