Closed mjafin closed 9 years ago
If you have access to our HPC in the US I can point you to the input data for debugging purposes.
Hi!
Show me your launch command line please.
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
We have placed fix and new build zip into the repository. Try it.
Yep, works now, thanks! Will continue kicking the tyres
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:
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.