Hi Daniel, I have been implementing the GATK unified genotyper and I was having some issues. Occasionally I would get an error that the Java virtual machine would not start. I got around that by adding the Xmx3g parameter to the command line. I also added the -nt 3 because otherwise it's really slow on human data. --stdout "${output_log}" #for $i, $input_bam in enumerate( $reference_source.input_bams ): -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index #end for -p 'java -Xmx3g -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" -o "${output_vcf}" ##-o "out_vcf.txt" -et "NO_ET" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" #end if -nt 3 --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}" --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}" Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>