Hi,

I’ve installed the latest version (using GATK2.8-1) of the GATK2 wrapper here.  I’ve run into the following error:

##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does not exist.

I see via much googling that this error is due to a user input problem.  I’ve tried pointing the gatk2_picard_index.loc file in tool-data to the proper data files:

hg19 hg19    hg19    /software/packages/galaxy/data/picard/hg19.fa

where the following files exist:

hg19.dict

hg19.fa

hg19.fa.fai

I’m using a torque setup.  A bam file is being used as input.  After much trial and error I’ve been unable to figure out what I’m missing. 

None of the solutions on google apply to my situation.

Has anyone else run into this configuration problem and solved it?

Thanks,

-Sheldon

Sheldon Briand

NRC Research Computing Support Analyst

Research Computing Support / Soutien Informartique a la Recherche

Operations, Science Portfolio / Operations, Portefeuil des sciences

SSC-NRC / SPC-CNRC

Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford

Halifax, NS  B3H 3Z1

902 426-1677

sheldon.briand@ssc-spc.gc.ca