Gatk

Question: Gatk

7.0 years ago by

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

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modified 7.0 years ago by Daniel Blankenberg ♦♦ 1.7k • written 7.0 years ago by Metge, Franziska • 10

7.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 7.0 years ago by Jennifer Hillman Jackson ♦ 25k

7.0 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 COMMENT • link written 7.0 years ago by Daniel Blankenberg ♦♦ 1.7k

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