Open lpalomerol opened 6 years ago
hi I also had the same mistake. How did you solve it? thanks
I also got this error. cmd: java -jar ISOWN/bin/REFORMVCF_v1.0.jar -vcfFolder case/ -output case_out.emaf Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1 at com.Processing.processVcf(Processing.java:119) at com.runReformating.main(runReformating.java:39)
Maybe the difference of the vcf format between the demo and my case caused this error. Does the value in some column matter? Appreciate if anyone can point out this.
I also got the same error.
Did anyone find a way to correct this error?
any updates?
Hello again,
sorry for the insistence. My "16:10 issue" is related with the generation of the training set. I am trying to run generate_training_set dataset and java is breaking with this trace:
` Reformat files in '/home/idibell/Documentos/pipelines/8.pujana/20180716.pdx.mutect/results/20180725.install.isown.db/2.vcf2' to emaf ...
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1 at com.Processing.processVcf(Processing.java:119) at com.runReformating.main(runReformating.java:39)
Generate training data set for '/home/idibell/Documentos/pipelines/8.pujana/20180716.pdx.mutect/results/20180725.install.isown.db/2.vcf2' ...
Exception in thread "main" java.lang.NullPointerException at helper.Headers.(Headers.java:41)
at main.Generator.getVariant2samples(Generator.java:243)
at main.Generator.loadVariants(Generator.java:19)
at main.runGenerator.main(runGenerator.java:47)
`
What i am doing wrong?
My JAVA_HOME variable, btw is "/usr/lib/jvm/jre-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64"
Regards, Luis.