I am trying to incorporate GATK in my pipeline but not been able to make it 
work. I aligned my data with Hg 19 and then ran sam tool filter and then picard 
duplicate removal. I uploaded dbSNP and the reference FASTA file for Hg 19 in 
galaxy to run this pipeline. But for some reason GATK tool for base 
recalibration will not accept this output file. I wonder if there is sorting or 
indexing issue but how to fix this in galaxy.

An error occurred running this job: Picked up _JAVA_OPTIONS: 
-Djava.io.tmpdir=/space/g2main [Mon Dec 10 10:30:42 EST 2012] 


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