Question: Error with "Realigner Target Creater" on Galaxy
gravatar for mht.tsai
3.8 years ago by
mht.tsai0 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: [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


galaxy • 1.0k views
ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson25k • written 3.8 years ago by mht.tsai0
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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:

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 COMMENTlink written 3.8 years ago by Jennifer Hillman Jackson25k
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