cramtools-2.1 out of memory error

[pandu_sait]

Hi all,
I am new to compression of sequence data.
when i am trying to compress the individual chromosome BAM file i am getting out of memory exception.
Input file used is ~88MB in size.

java -jar cramtools-2.1.jar cram -I NA19240.chrom1.sorted.bam.bam -R c                               hr1.fa -O test.cram
Exception in thread "main" java.lang.reflect.InvocationTargetException
     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:606)
     at net.sf.cram.CramTools.invoke(CramTools.java:93)
     at net.sf.cram.CramTools.main(CramTools.java:123)
Caused by: java.lang.OutOfMemoryError: Java heap space
     at java.util.Arrays.copyOf(Arrays.java:2271)
     at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:118)
     at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
     at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
     at net.sf.cram.io.ByteBufferUtils.copyLarge(ByteBufferUtils.java:615)
     at net.sf.cram.io.ByteBufferUtils.readFully(ByteBufferUtils.java:623)
     at net.sf.cram.ref.ReferenceSource.loadFromPath(ReferenceSource.java:253)
     at net.sf.cram.ref.ReferenceSource.findBasesByMD5(ReferenceSource.java:283)
     at net.sf.cram.ref.ReferenceSource.findBases(ReferenceSource.java:179)
     at net.sf.cram.ref.ReferenceSource.getReferenceBases(ReferenceSource.java:127)
     at net.sf.cram.FixBAMFileHeader.fixSequence(FixBAMFileHeader.java:54)
     at net.sf.cram.FixBAMFileHeader.fixSequences(FixBAMFileHeader.java:47)
     at net.sf.cram.Bam2Cram.main(Bam2Cram.java:307)
     ... 6 more

Though, I could succesfully run cram by explicitly setting java memory size directives ( -Xms256m -Xmx2048m)
if for smaller files itself cramtools reports "Out of memory", how to run cramtools for larger files

Could anyone help me understand how to work with cramtools on larger files.

Thanks,
Pandu Kumar C

[Brian Bushnell]

The error you are getting is from running out of memory... so, I would assume that you need more than 2048MB. Note that you will get the best memory efficiency if you set -Xms and -Xmx to the same value. But you probably still need more. Bam files are already compressed, so you can get an idea of the upper limit of how much memory should be needed (excluding overhead) by converting them to sam. I don't know what kind of overhead cramtools needs.