Hi Umar,
Can you click the eye icon to view the contents of the 'log' dataset for the
GATK run. The end of the log should have the actual error encountered (the text
you provided is a bit of a red herring)
Since you are using hg19, the most likely cause for the error is that the
reference fasta file you are using is not ordered properly, or that your
alignments were made using a different genome (e.g. alignment with bwa using
built-in hg19 [not ordered properly] and then GATK using a different hg19 fasta
from your history.)
If you are using a custom genome, make sure that it is GATK-ordered and that
the same one is used in all steps; there is an hg19 GATK-ordered fasta file
available in a Data library ('GATK') on Main.
Thanks for using Galaxy,
Dan
On Dec 11, 2012, at 12:11 PM, Farooq,Umar (res) wrote:
> Hi,
>
> 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]
> net.sf.picard.sam.CreateSequenceDictionary
> REFERENCE=/space/g2main/tmp-gatk-tKp41A/gatk_input.fasta
> OUTPUT=/space/g2main/tmp-gatk-tKp41A/dict3503196447953523717.tmp
>
> Thanks,
> Umar
>
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___________________________________________________________
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