Dear GenomeSTRiP developer,
I've run the svdiscovery script and it hangs on after all individual SV detection finished. The error message I've got is the following:
INFO 23:14:42,482 HelpFormatter - -------------------------------------------------------------
INFO 23:14:42,484 HelpFormatter - Program Name: org.broadinstitute.sv.apps.MergeDiscoveryOutput
INFO 23:14:42,487 HelpFormatter - Program Args: -O /home/lin017/nobackup/gs_output/output.sites.unfiltered.vcf
INFO 23:14:42,488 HelpFormatter - Date/Time: 2013/07/30 23:14:42
INFO 23:14:42,488 HelpFormatter - -------------------------------------------------------------
INFO 23:14:42,488 HelpFormatter - -------------------------------------------------------------
Exception in thread "main" java.lang.RuntimeException
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:46)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:24)
at org.broadinstitute.sv.apps.MergeDiscoveryOutput.main(MergeDiscoveryOutput.java:40)
Caused by: java.lang.NullPointerException
at org.broadinstitute.sv.common.RunFileMerger.guessPartitionList(RunFileMerger.java:93)
at org.broadinstitute.sv.common.RunFileMerger.merge(RunFileMerger.java:78)
at org.broadinstitute.sv.common.RunFileMerger.merge(RunFileMerger.java:73)
at org.broadinstitute.sv.apps.MergeDiscoveryOutput.run(MergeDiscoveryOutput.java:51)
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:38)
... 4 more
Thanks in advance.
Regards,
Ke Lin