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}" "${input_bam.input_bam.ext}" 
       -d "" "${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

Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.com<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Reply via email to