Hi Team,

I have installed GATK2 into a galaxy cloud instance to use the Unified Genotyper for our sequencing course. However, when I run the tool I get the following error message:

Dataset 41: Unified Genotyper on data 8 and data 13 (VCF)

Tool execution generated the following error message:

ERROR ------------------------------------------------------------------------------------------ ERROR A USER ERROR has occurred (version 3.2-2-gec30cee): ERROR ERROR This means that one or more arguments or inputs in your command are incorrect. ERROR The error message below tells you what is the problem. ERROR ERROR If the problem is an invalid argument, please check the online documentation guide ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool. ERROR ERROR Visit our website and forum for extensive documentation and answers to ERROR commonly asked questions http://www.broadinstitute.org/gatk ERROR ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself. ERROR ERROR MESSAGE: Invalid argument value '/mnt/galaxy/tools/gatk2/bin/' at position 8. ERROR ------------------------------------------------------------------------------------------

The following is the command that is being invoked by galaxy:

python /mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/84584664264c/gatk2/gatk2_wrapper.py --stdout "/mnt/galaxy/files/000/dataset_326.dat" -d "-I" "/mnt/galaxy/files/000/dataset_226.dat" "bam" "gatk_input_0" -d "" "/mnt/galaxy/files/_metadata_files/000/metadata_13.dat" "bam_index" "gatk_input_0" -p ' java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" --num_threads ${GALAXY_SLOTS:-4} --out "/mnt/galaxy/files/000/dataset_324.dat" --metrics_file "/mnt/galaxy/files/000/dataset_325.dat" $GATK2_SITE_OPTIONS --num_cpu_threads_per_data_thread 1 --genotype_likelihoods_model "BOTH" --standard_min_confidence_threshold_for_calling "30.0" --standard_min_confidence_threshold_for_emitting "30.0" ' -d "-R" "/mnt/galaxy/files/000/dataset_220.dat" "fasta" "gatk_input"

I have reviewed my configuration files and cannot locate where the issue lies. I am also posting this with the GATK Forum to see if they have any ideas. Unfortunately I need to get this resolved ASAP since I need to complete my testing by tomorrow.

Thanks,

Iry

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