Hi Yan,
This is not enough information to give you a solution, but there are a
few ways to investigate the problems or submit it to use for feedback.
Is this error on the public Galaxy server at https://main.g2.bx.psu.edu
(usegalaxy.org)? Of so, you can submit a bug report of the problem and
we can provide help. Please make certain the input and error datasets
are left undeleted.
http://wiki.galaxyproject.org/Support#Reporting_tool_errors
The tool can produce errors for many reasons, but they are generally due
to input formatting or missing required inputs required by certain
annotations. If you are running this on a cloud or local Galaxy, or even
on the public Main server, clicking on the bug icon will reveal the
entire error message. The specific problem is included with these error
messages in the majority of cases. Often this can be mapped back to the
GATK documentation and the input problems resolved.
Best,
Jen
Galaxy team
On 9/25/13 1:11 AM, Yan He wrote:
Hi all,
I am analyzing some targeted resequencing data. I was trying to use
Variant Annotation tool under GATK after got .VCF file. But some error
as following returned. Would you please help me to figure out what
happened? Or this tool can only be used for some model organisms?
Thanks a lot!
"An error occurred with this dataset: /Picked up _JAVA_OPTIONS:
-Djava.io.tmpdir=/space/g2main [Wed Sep 25 03:59:41 EDT 2013]
net.sf.picard.sam.CreateSequenceDictionary
REFERENCE=/space/g2main/tmp-gatk-4SDjhY/gatk_input.fasta
OUTPUT=/space/g2main/tmp-gatk-4SDjhY/dict5123971853428830433.tmp"/
//
/Yan/
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
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
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
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/
