Hello all, one of my users encounters a strange error with the GATK tool "Unified Genotyper". At the end of the message you see the original error report. The problem there was that the reference genome is missing. The tool was run as a part of a bigger workflow, but I double checked the workflow and the correct genome is specified there. All other GATK tools work, so there should be no error with the setup of the locally cached references. When I use the rerun button in Galaxy to repeat this step (without changing anything), everything works fine. Best regards, Sarah ----- Forwarded Message ----- From: diehl@immunbio.mpg.de To: diehl@immunbio.mpg.de, barenboim@immunbio.mpg.de Sent: Friday, August 10, 2012 10:08:12 AM Subject: Galaxy tool error report from barenboim@immunbio.mpg.de GALAXY TOOL ERROR REPORT ------------------------ ----------------------------------------------------------------------------- job id: 20471 tool id: gatk_unified_genotyper ----------------------------------------------------------------------------- job command line: python /galaxy/galaxy_server/tools/gatk/gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "/galaxy/galaxy_server/database/files/023/dataset_23795.dat" -d "-I" "/galaxy/galaxy_server/database/files/023/dataset_23792.dat" "bam" "gatk_input_0" -d "" "/galaxy/galaxy_server/database/files/_metadata_files/001/metadata_1060.dat" "bam_index" "gatk_input_0" -p 'java -jar "/galaxy/galaxy_server/tool-data/shared/jars/gatk/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" --num_threads 4 --out "/galaxy/galaxy_server/database/files/023/dataset_23793.dat" --metrics_file "/galaxy/galaxy_server/database/files/023/dataset_23794.dat" -R "" --genotype_likelihoods_model "BOTH" --standard_min_confidence_threshold_for_calling "30.0" --standard_min_confidence_threshold_for_emitting "30.0" ' -d "--dbsnp:dbsnp,%(file_type)s" "/galaxy/galaxy_data/gatk/b37/dbsnp_135.b37.vcf" "vcf" "input_dbsnp_0" ----------------------------------------------------------------------------- job stderr: ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 1.6-13-g91f02df): ##### 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/tmp-gatk-eEVeYq) does not exist. ##### ERROR ------------------------------------------------------------------------------------------ ----------------------------------------------------------------------------- job stdout: ----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).