Question: Error with "Realigner Target Creater" on Galaxy
gravatar for mht.tsai
3.3 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 • 888 views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.3 years ago by mht.tsai0
gravatar for Jennifer Hillman Jackson
3.3 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 3.3 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 86 users visited in the last hour