Question: Gatk
0
gravatar for Metge, Franziska
6.2 years ago by
Metge, Franziska10 wrote:
Dear happy users of Galaxy, We are running Galaxy locally. It's a very fine tool! By now everything works fine, except when I try to run any GATK program. I usually get this error message: ##### ERROR ---------------------------------------------------------- -------------------------------- ##### ERROR A USER ERROR has occurred (version 1.3-14-g348f2db): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: The fasta file you specified (/tmp/tmpp0oxJu/hg19) does not exist. ##### ERROR ---------------------------------------------------------- -------------------------------- my picard_index.loc line for the hg19 reference looks like this: hg19 hg19 hg19 hg19 /drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa gatk also the bam file I am submitting to GATK has the reference genome specified in it's attributes. Could please anyone help me. Thank you Franzi
galaxy • 993 views
ADD COMMENTlink modified 6.2 years ago by Daniel Blankenberg ♦♦ 1.7k • written 6.2 years ago by Metge, Franziska10
0
gravatar for Jennifer Hillman Jackson
6.2 years ago by
United States
Jennifer Hillman Jackson23k wrote:
Hi Metge, Thank you for your kind comments! The GATK tool wrappers are still in an early beta stage of development. Because of this, we are not ready to support set-up in local instances yet. If you have functionality input for the version on our Test server, general feedback is welcomed on the galaxy-dev@bx.psu.edu mailing list. Take care, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENTlink written 6.2 years ago by Jennifer Hillman Jackson23k
0
gravatar for Daniel Blankenberg
6.2 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:
Hi Franzi, You have one too many hg19 in there. The fields go like: <unique_build_id> <dbkey> <display_name> <fasta_file_path> <valid_tool_suites> so: hg19 hg19 hg19 /drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa gatk But do note that these tool integrations are still undergoing active development. Please report bugs if you encounter any. Thanks for using Galaxy, Dan
ADD COMMENTlink written 6.2 years ago by Daniel Blankenberg ♦♦ 1.7k
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