Bowtie2 mm9 index
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
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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-- Jennifer Hillman-Jackson http://galaxyproject.org
Hi Mary, The data was restored this morning. Good luck with the new run, Jen Galaxy team On 11/7/13 2:57 PM, Jennifer Jackson wrote:
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jackson http://galaxyproject.org
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jackson http://galaxyproject.org
participants (2)
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Davis, Mary -
Jennifer Jackson