I can get Apollo to load a 14mb fasta file with GFF annotation on Win XP
Pro, but it dies when I try to load a 23mb fasta file. The error log shows
;
Exception in thread "Thread-4" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Unknown Source)
at java.lang.AbstractStringBuilder.expandCapacity(Unknown Source)
at java.lang.AbstractStringBuilder.append(Unknown Source)
at java.lang.StringBuffer.append(Unknown Source)
at apollo.seq.io.FastaFile.parse(FastaFile.java:180)
at apollo.seq.io.FastaFile.processReader(FastaFile.java:60)
at apollo.seq.io.FastaFile.<init>(FastaFile.java:71)
at
apollo.dataadapter.gff3.GFF3Adapter.parseSeq(GFF3Adapter.java:408)
at
apollo.dataadapter.gff3.GFF3Adapter.parseSeq(GFF3Adapter.java:422)
at
apollo.dataadapter.gff3.GFF3Adapter.getCurationSet(GFF3Adapter.java:143)
at
apollo.dataadapter.gff3.GFF3AdapterGUI.doOperation(GFF3AdapterGUI.java:198)
at
org.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdapterC
hooser.java:361)
at
apollo.main.DataLoader$ApolloAdapterChooser.doCommit(DataLoader.java:750)
at
org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChoos
er.java:136)
at java.lang.Thread.run(Unknown Source)
Apollo will not start if the Apollo.vmoptions file is in the root directory,
so I can't try to adjust the Java memory size. Changing the memory size in
the Apollo.conf file seems to have no effect. The same thing happens on my
Win 7 64 machine. The XP machine has 4gb (3.25gb usable) and the Win 7
machine has 16gb so I don't think its actually running out of memory. Is
this standard behavior? We'd love to use Apollo in our lab's annotation
effort but the most of our reference sequences are at least 15mb. Any
suggestions?
Thanks,
Ed
Virgil Ed Johnson
Scientific Computing Professional Principle
Tsai Laboratory
Warnell School of Forestry
University of Georgia
706-542-4743
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