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ridgelab / ssva

Splice Site Variant Analyzer
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Error: java.lang.IndexOutOfBoundsException: Index: 1, Size: 0 #1

Open lihb001 opened 5 years ago

lihb001 commented 5 years ago

Hi Developers, I meet some error when runing ssva. I thinks this may be a bug, so I need you help.

I run command as below: $ java -jar /work/Software/SSVA-1.0/target/SSVA-1.0-jar-with-dependencies.jar -i /mnt/resource/lihb_project/tmp/test/test.combined.vcf -o /mnt/resource/lihb_project/tmp/test/Splicing -a /work/Software/annovar_2018-04-16 -d /work/Database/Annovar_db/hg38_20180130 -b hg38 -g /work/Database/GATK_db/Other_RefGenome/hg38_rmContig/Split_Chr -m /work/Software/SSVA-1.0/MES

Existing avinput file found: test.combined.vcf.avinput Running Gene Annotation Running 1000 Genomes MAF Annotation Running Exac Annotation Running dbscSNV Annotation Going through the variants [. ] 3.18%java.lang.IndexOutOfBoundsException: Index: 1, Size: 0 at java.util.ArrayList.rangeCheck(ArrayList.java:657) at java.util.ArrayList.get(ArrayList.java:433) at analyzer.variantInfo.Variant.parseSpliceInfo(Variant.java:210) at analyzer.SpliceRunner.run(SpliceRunner.java:104) at analyzer.SpliceEngine.main(SpliceEngine.java:24)

The tempory avinput file as below: test.combined.vcf.zip

Thanks!

ridgelab commented 5 years ago

We've updated SSVA with a patch that should address this issue. Please let us know if you are still experiencing the error.

lihb001 commented 5 years ago

Hi Developers, I run git clone the ssva, and reinstall.

Then I run command as below, but the result file is empty.

$ java -jar /work/Software/SSVA-1.0/target/SSVA-1.0-jar-with-dependencies.jar -i /mnt/resource/lihb_project/tmp/test/test.combined.vcf -o /mnt/resource/lihb_project/tmp/test/Splicing -a /work/Software/annovar_2018-04-16 -d /work/Database/Annovar_db/hg38_20180130 -b hg38 -g /work/Database/GATK_db/Other_RefGenome/hg38_rmContig/Split_Chr -m /work/Software/SSVA-1.0/MES/ Existing avinput file found: test.combined.vcf.avinput Existing .variant_function file found: test.combined.vcf.avinput.variant_function Running 1000 Genomes MAF Annotation Running Exac Annotation Running dbscSNV Annotation Going through the variants [..................................................] 100.00%

Result directory: Splicing.tar.gz

ridgelab commented 5 years ago

We've updated SSVA with another patch. Please let us know if this is still an issue.

lihb001 commented 5 years ago

Hi Developers! I reinstall SSVA and run command as before, but the result file is also empty without error reported.

Could you share me a test vcf file that you have test successfully.

Now I confuse what the matter happen to me.

$ java -jar /work/Software/SSVA-1.0/target/SSVA-1.0-jar-with-dependencies.jar -i /mnt/resource/lihb_project/tmp/test/test.combined.vcf -o /mnt/resource/lihb_project/tmp/test/Splicing -a /work/Software/annovar_2018-04-16 -d /work/Database/Annovar_db/hg38_20180130 -b hg38 -g /work/Database/GATK_db/Other_RefGenome/hg38_rmContig/Split_Chr -m /work/Software/SSVA-1.0/MES Existing avinput file found: test.combined.vcf.avinput Existing .variant_function file found: test.combined.vcf.avinput.variant_function Running 1000 Genomes MAF Annotation lRunning Exac Annotation Running dbscSNV Annotation Going through the variants [..................................................] 100.00%