Hey everybody,

At the moment I try to index a bunch of sequences with malt. I've indexed all viral proteins from refseq without a problem. But now I wanted to index all bacterial ref-seq sequences at once. The file is about 9.8gb great and contains 5242 sequences. I used the command:

./malt-build -L /ifs/data/nfs_share/sukmb241/home.julian/malt/MEGAN5-academic-license.txt --input references/bacteriall_nucleotide --sequenceType DNA --index index/bacteriall_nr/

But after allocating the hash table the program spits out the following error:

Allocating: 75.6 GB
java.lang.OutOfMemoryError: Java heap space
        at java.nio.HeapByteBuffer.<init>(Unknown Source)
        at java.nio.ByteBuffer.allocate(Unknown Source)
        at jloda.E.H.<init>(Unknown Source)
        at jloda.E.D.<init>(Unknown Source)
        at malt.data.O.A(Unknown Source)
        at malt.MaltBuild.run(Unknown Source)
        at malt.MaltBuild.main(Unknown Source)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
        at java.lang.reflect.Method.invoke(Unknown Source)
        at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
        at com.install4j.runtime.launcher.UnixLauncher.main(Unknown Source)

I changed the -Xmx parameter in the vmoptions files as described in the manual and my last try to get this to work was with 120g but it crashed with the exact same error message as above. At the moment I have no way to increase the memory level. Has anybody experience with the indexing of greater files in Malt? Did you encounter the same problem?

With best regards and thanks in advance,

Julian