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Question: Error with "Realigner Target Creater" on Galaxy
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gravatar for mht.tsai
3.8 years ago by
mht.tsai • 0
Australia
mht.tsai • 0 wrote:

I used Realigner Target Creater on Galaxy with GATK --> ucsc.hg19.fasta and Mills and 1000G gold starndard.indels.hg19.vcf but showed an error as follows:

Where did I do wrong?

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch [Thu Feb 12 09:24:55 CST 2015] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/galaxy-repl/main/scratch/tmp-gatk-fH2NY7/gatk_input.fasta OUTPUT=/galaxy-repl/main/scratch/tmp-gatk-f

Hank
galaxy • 1.0k views
ADD COMMENT • link •
modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by mht.tsai • 0
0
gravatar for Jennifer Hillman Jackson
3.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There may be an input problem - perhaps a reference genome mismatch issue, but that can be checked. Help is here to do that, section 2.11:
http://wiki.galaxyproject.org/Support

Also, it sounds as if you are working on the public Main Galaxy instance. If so, or if you can duplicate the error, and have eliminated a reference genome mismatch problem, please send in a bug report from the error dataset, we can help to troubleshoot.

Best, Jen, Galaxy team
ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
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