title: Java VM fails with heap size increase
body: <p>S0 the command I am trying to run is;</p>
  
  <pre><code>java -jar -Xmx290G  /ibers/ernie/home/thh32/rumenISPG/GenomeAnalysisTK.jar  -T VariantFiltration -R Contigs_1.fa  -V Rank10_clean.fasta.gz.Contig_1-sort.bam.vcf1.vcf  --filterExpression "QD &lt; 2.0 || FS &gt; 60.0 || MQ &lt; 40.0 || HaplotypeScore &gt; 13.0 || MappingQuality RankSum &lt; -12.5 "  --filterName "testing_filter"  -o filtered_snps.vcf
  </code></pre>
  
  <p>The machine I am running it on has access to 500G RAM so shouldnt be an issue, however I keep getting this error message;</p>
  
  <pre><code>Error occurred during initialization of VM
  Unable to allocate 9502720KB bitmaps for parallel garbage collection for the requested 304087040KB heap.
  Error: Could not create the Java Virtual Machine.
  Error: A fatal exception has occurred. Program will exit.
  </code></pre>
  
  <p>Has anyone else experienced this issue and if so did you resolve it?</p>
  
  <p>Oh also just incase people wonder why I am giving this program so much memory, when I didnt I got this message which indicates that it needs more RAM. This was with 100G heaps size.</p>
  
  <pre><code>INFO  09:55:57,953 HelpFormatter - --------------------------------------------------------------------------------- 
  INFO  09:55:57,955 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12 
  INFO  09:55:57,956 HelpFormatter - Copyright (c) 2010 The Broad Institute 
  INFO  09:55:57,956 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
  INFO  09:55:57,961 HelpFormatter - Program Args: -T VariantFiltration -R Contigs_1.fa -V Rank10_clean.fasta.gz.Contig_1-sort.bam.vcf1.vcf --filterExpression QD &lt; 2.0 || FS &gt; 60.0 ||
   MQ &lt; 40.0 || HaplotypeScore &gt; 13.0 || MappingQuality RankSum &lt; -12.5  --filterName testing_filter -o filtered_snps.vcf 
  INFO  09:55:57,967 HelpFormatter - Executing as thh32@node011 on Linux 2.6.32-504.30.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_40-b26. 
  INFO  09:55:57,968 HelpFormatter - Date/Time: 2015/10/27 09:55:57 
  INFO  09:55:57,968 HelpFormatter - --------------------------------------------------------------------------------- 
  INFO  09:55:57,969 HelpFormatter - --------------------------------------------------------------------------------- 
  INFO  09:55:58,474 GenomeAnalysisEngine - Strictness is SILENT 
  ##### ERROR ------------------------------------------------------------------------------------------
  ##### ERROR A USER ERROR has occurred (version 3.4-46-gbc02625): 
  ##### 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: There was a failure because you did not provide enough memory to run this program.  See the -Xmx JVM argument to adjust the maximum heap size provided to Java
  ##### ERROR ------------------------------------------------------------------------------------------
  </code></pre>
  
  <p>Thanks,
  Tom</p>