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

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

 --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.



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