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Integrative-Transcriptomics / MUSIAL

Summarize SNV and indel information on single gene or genome level together with other relevant statistics based on .vcf files.
https://tuevis.cs.uni-tuebingen.de/musial/
GNU General Public License v3.0
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SNPEff error #4

Closed JudithNeukamm closed 5 years ago

JudithNeukamm commented 5 years ago

I always get an error when running SNPEff: SNPEffCommand: java -jar snpEff.jar mySample snvVcfForSnpEff.vcf Exception in thread "main" java.lang.NullPointerException at datastructure.SNVTable.toStringWithSNPEffInfos(SNVTable.java:412) at tools.Analyzer.run(Analyzer.java:558) at tools.Analyzer.(Analyzer.java:394) at main.Musial.main(Musial.java:27)

alex-seitz commented 5 years ago

If you run it without snpeff, does it work without errors and do you get a result?

JudithNeukamm commented 5 years ago

It works perfect without snpeff.

alex-seitz commented 5 years ago

Strange, I ran several tests here and can't reproduce the error, can you maybe give me access to a minimum test dataset where the error occurs?

Thank you

JudithNeukamm commented 5 years ago

Hi Alex,

sorry for the late response. I tried it on some published T. pallidum genomes (CDC2, Gauthier, DAL-1, and Chicago) and I get the same error as with the leprosy genomes before. I can send you the data directly if you wish.

Best, Judith

JudithNeukamm commented 5 years ago

Hm it worked now. It could have been a problem with the naming. But thanks for checking :)