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
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/
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Yan He