Virmid - SNV mutation caller

shyam_la · 05-08-2014, 01:07 PM

Anyone here have any experience using Virmid? I have some exome seq data that I want to use it on but on first attempt with default parameters I get this error:

Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String ind
ex out of range: -1
at java.lang.String.substring(Unknown Source)
at virmid.Param.reportFile(Param.java:225)
at virmid.Virmid.main(Virmid.java:112)

Any ideas?

shyam_la · 05-13-2014, 07:36 AM

For everyone's info, I contacted the developers.

The issue was because I was using Windows and they had a bug that confused forward vs backward slashes in path names. They fixed it and released a new version 1.1.1 and it works fine now.

kevinrue · 02-16-2017, 07:34 AM

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:

Code:

Exception in thread "main" java.lang.NullPointerException
	at virmid.Virmid.callFinalVariants(Virmid.java:1116)
	at virmid.Virmid.main(Virmid.java:150)

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,
Kevin

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05-08-2014, 01:07 PM	#1
shyam_la Member Location: California Join Date: Mar 2012 Posts: 97	Virmid - SNV mutation caller Anyone here have any experience using Virmid? I have some exome seq data that I want to use it on but on first attempt with default parameters I get this error: Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String ind ex out of range: -1 at java.lang.String.substring(Unknown Source) at virmid.Param.reportFile(Param.java:225) at virmid.Virmid.main(Virmid.java:112) Any ideas?

02-16-2017, 07:34 AM	#3
kevinrue Member Location: London Join Date: Jan 2013 Posts: 25	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: Code: Exception in thread "main" java.lang.NullPointerException at virmid.Virmid.callFinalVariants(Virmid.java:1116) at virmid.Virmid.main(Virmid.java:150) 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, Kevin

05-13-2014, 07:36 AM	#2
shyam_la Member Location: California Join Date: Mar 2012 Posts: 97	For everyone's info, I contacted the developers. The issue was because I was using Windows and they had a bug that confused forward vs backward slashes in path names. They fixed it and released a new version 1.1.1 and it works fine now.