ArrayIndexOutOfBoundsException when generating training set

[lpalomerol]

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.

[solivehong]

hi
I also had the same mistake. How did you solve it?
thanks

[renyongzhe]

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.

[itamuria]

I also got the same error.

[amit21AIT]

Did anyone find a way to correct this error?

[slavnycoder]

any updates?