You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
got error
DEBUG 2021-11-12 13:14:59 BlockCompressedOutputStream Using deflater: Deflater
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:127)
at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:190)
at BamPrinter.printBAM(BamPrinter.java:321)
at Mapper.run(Mapper.java:574)
at VirGenA.main(VirGenA.java:31)
The text was updated successfully, but these errors were encountered:
Hello! Sorry for the late answer: I've missed the question somehow. Have you tried adding -Xmx30G option to java? By default it use only 4Gb. The full command will look like:
I have run the tool as follows with ram of 35 gb
java -jar VirGenA.jar map -c config_copy.xml
got error
DEBUG 2021-11-12 13:14:59 BlockCompressedOutputStream Using deflater: Deflater
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:127)
at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:190)
at BamPrinter.printBAM(BamPrinter.java:321)
at Mapper.run(Mapper.java:574)
at VirGenA.main(VirGenA.java:31)
The text was updated successfully, but these errors were encountered: