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ikalatskaya / ISOWN

Apache License 2.0
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ArrayIndexOutOfBoundsException when generating training set #13

Open lpalomerol opened 6 years ago

lpalomerol commented 6 years ago

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 commented 5 years ago

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

renyongzhe commented 5 years ago

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 commented 5 years ago

I also got the same error.

amit21AIT commented 5 years ago

Did anyone find a way to correct this error?

slavnycoder commented 4 years ago

any updates?