Exception in thread "main" java.lang.NullPointerException

[mjafin]

Hi, I'm testing VarDict Java on bcbio-nextgen's integration test data and it's dying out on me likely due to edge cases:

Exception in thread "main" java.lang.NullPointerException
        at com.astrazeneca.vardict.VarDict.toRegions(VarDict.java:101)
        at com.astrazeneca.vardict.VarDict.start(VarDict.java:64)
        at com.astrazeneca.vardict.Main.run(Main.java:135)
        at com.astrazeneca.vardict.Main.main(Main.java:24)

When running VarDict (the perl version) it often throws missing variable warnings (but doesn't die out). I suspect this would cause the Java version to crash though if it's trying to access variables that don't exist. I'm just guessing here since the error message isn't very verbose.

[mjafin]

If you have access to our HPC in the US I can point you to the input data for debugging purposes.

[ghost]

Hi!

Show me your launch command line please.

[mjafin]

Here's what I ran in the US:

. /group/ngs/bin/bcbio.sh 0.8.7

/group/ngs/share/VarDictInstall/VarDictJava/build/install/VarDict/bin/VarDict \
-G /gpfs/users/klrl262/dev/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -f 0.1 -N c-tumor \
-b /gpfs/users/klrl262/dev/bcbio-nextgen/tests/test_automated_output/align/c-tumor/1_2014-02-05_tcancer2-sort.bam \
-c 1 -S 2 -E 3 -g 4 \
/users/klrl262/dev/bcbio-nextgen/tests/test_automated_output/vardict/chr22/PairedBatch-chr22_0_20001-raw-unmerged-regions.bed \
> javaunpaired.txt

[ghost]

We have placed fix and new build zip into the repository. Try it.

[mjafin]

Yep, works now, thanks! Will continue kicking the tyres