Forum Login Issue:
Currently the "Log in with Google" button redirects you to a "Page not found." This is an issue that our forum vendors are working on fixing. In the meantime, while on the "Page not found" you can edit the URL to delete the second gatk, firecloud, or wdl (depending on what subforum you are acessing).
ex: https://gatkforums.broadinstitute.org/gatk/gatk/entry/...

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)

Best Answer

Answers

Sign In or Register to comment.