Sg-Adviser Exception In Thread "Pool-2-Thread-1" Java.Lang.Arrayindexoutofboundsexception

Question

[vlad1]

it returns error when I try to open native genome annotation file with suggested coding and splising variant filter

C:\Users\vmorozov>java -showversion java version "1.7.0_06" Java(TM) SE Runtime Environment (build 1.7.0_06-b24) Java HotSpot(TM) 64-Bit Server VM (build 23.2-b09, mixed mode)

C:\downloads\SG-Adviser_UI\SG-Adviser_UI>java -Xmx6g -jar SG-ADVISER_UI_1.6_5.ja r File size is: 981963108352 SG-Adviser UI_1.6_5 Filelenght is: 5619251200 File lenght in gb is 5.0 Filelenght is: 5619251200 Exception in thread "pool-2-thread-1" java.lang.ArrayIndexOutOfBoundsException: 12 at ScrippsGenomeAdviserUI.FilterFunctions.prefilter(FilterFunctions.java :1465) at ScrippsGenomeAdviserUI.FilterFunctions.run(FilterFunctions.java:2211)

    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

Answer 1

[galina.erikson]

Hi vmmorozov,

I'm the developer of the SG-ADVISER UI and I will attempt to help you with this problem. The tool is created to accept only SG Adviser annotated files. One of the problems might be that you tried to insert something else other then a file annotated by SG Adviser (vcf, masterVar). Can you please sent me the header line plus the first few lines in the file you attempted to insert into the tool? To annotate your file using sg-adviser you will have to create an username and upload the file through the web. If you don't have a *.edu email address please PM me your email and I can create an account for you. Once you get the SG Adviser annotated file you can then use the UI to filter and analyze your file.

Thank you,

-Galina