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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

CreateSequenceDictionary OutOfMemoryError

I'm running CreateSequenceDictionary on a Windows 10 machine with 4 gigabytes of ram and more than 50 gigabytes of free disk space, while my human dna reference file is nearly 3 gigabytes. The same problem does not appear whenever I use a very small fasta file made for demonstration purposes and the dict is normally created. Here's the error I keep getting

Runtime.totalMemory()=259522560
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:185)
at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSequence(IndexedFastaSequenceFile.java:164)
at htsjdk.samtools.reference.IndexedFastaSequenceFile.nextSequence(IndexedFastaSequenceFile.java:241)
at picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:141)
at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:121)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
at picard.sam.CreateSequenceDictionary.main(CreateSequenceDictionary.java:97)

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