Holiday Notice:
The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!

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

To get help, see
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(
at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSequence(
at htsjdk.samtools.reference.IndexedFastaSequenceFile.nextSequence(
at picard.sam.CreateSequenceDictionary.makeSequenceDictionary(
at picard.sam.CreateSequenceDictionary.doWork(
at picard.cmdline.CommandLineProgram.instanceMain(
at picard.sam.CreateSequenceDictionary.main(

Best Answer


Sign In or Register to comment.