Error in b2g4pipe

Question

[CikLa]

Hi,

I run a b2g4pipe analysis which I feed blast xml file and interproscan xml file. Both were run in my cluster computer. When I run b2g4pipe through bash script, I got this error:

Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit
        at java.util.Arrays.copyOf(Arrays.java:2367)
        at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
        at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:
114)
        at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:415)
        at java.lang.StringBuffer.append(StringBuffer.java:237)
        at es.blast2go.prog.blast.ParseBlastXml.parse(ParseBlastXml.java:125)
        at es.blast2go.prog.blast.ParseBlastXml.parseFile(ParseBlastXml.java:77)
        at es.blast2go.prog.B2GAnnotPipe.<init>(B2GAnnotPipe.java:199)
        at es.blast2go.prog.B2GAnnotPipe.main(B2GAnnotPipe.java:102)

I believe this is something about the memory here. Even by using -Xmx40000m it still give such error message. Anyone mind to help?

Thanks

Answer 1

[thiagomafra]

Hello,

Maybe it is because the version of blastx when you generate the .xml file. The newest version doesn't work well. Try to run blastx in old version (2.2.19), remember to reformat your database with formatdb.

[CikLa]

I already run blastp which the database was formatted using formatdb. I think that would be no problem. It succeed with smaller size of xml file. Or can I split the xml file. But if so, how to get overall representation of my dataset?