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Old 02-16-2017, 06:34 AM   #3
Location: London

Join Date: Jan 2013
Posts: 25
Default Virmid 1.2.0 systematically fails at function "callFinalVariants"

Dear all,

I have been trying the latest Virmid 1.2.0 (released 2015-07-14) under a range of settings, all of which fail with the following error message:

Exception in thread "main" java.lang.NullPointerException
	at virmid.Virmid.callFinalVariants(
	at virmid.Virmid.main(
I have posted the issue on the SourceForge repository, following up on Irantzu Anzar who also reported a similar (yet different) error message a month ago, without any reply yet.

I have also tried to investigate the source of the error myself, from the available source code on the same SourceForge repository. However, the available source code (on both SourceForge and the linked git repository) was last updated on 2013-08-20. Obviously, that old code release does not match the lines that throw the errors, both in my case and that of Irantzu.

If anyone knows where the latest code is (updates between 2013 and the latest release in 2015), I'd be happy to have a look.
Otherwise, advice from anyone with recent experience of Virmid is more than welcome. I wish to compare Virmid with other somatic variant callers that work perfectly on the same input files.

Best regards,
kevinrue is offline   Reply With Quote