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ikalatskaya / ISOWN

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Error when converting VCF file to emaf #23

Open itamuria opened 5 years ago

itamuria commented 5 years ago

Dear Irina,

I got an error in the 3rd step when I had to convert VCF files to emaf file.

I used this command: perl ${ISOWN_HOME}/bin/run_isown.pl ./annovar_results ./isown_results/test.output.txt " -trainingSet ${ISOWN_HOME}/training_data/BRCA_100_TrainSet.arff -sanityCheck false -classifier nbc"

And I got this error:

Reformat files in '/home/ISOWN/annovar_results' to emaf ... Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1 at com.Processing.processVcf(Processing.java:119) at com.runReformating.main(runReformating.java:39)

As I didn't get any information about the error it is difficult to know what can we do. I would appreciate any feedback.

Thanks, All the best, Ibon

amit21AIT commented 5 years ago

@itamuria I am also getting the same error when i tried converting VCF to emaf . Did you find a way to correct it ?

itamuria commented 5 years ago

Dear @amit21AIT, I am in contact with the authors but they haven't provided any resolutive answer. I will let you know if I solve it.

amit21AIT commented 5 years ago

@itamuria i found a way to correct this error , annovar is using hg19 by default but i used hg38 for alignment so i downloaded the hg38.fa file and used -buildver hg38 parameter in all 3 lines of annovar_annotation.pl file and again did database annotation and now its running fine . Also check whether your annotated vcf file is proper or not , like in my case one of the column name was '1' so i changed it to 'TUMOR' and its working now no errors. Hope it helps. Thanks

peishimei commented 5 years ago

@itamuria i found a way to correct this error , annovar is using hg19 by default but i used hg38 for alignment so i downloaded the hg38.fa file and used -buildver hg38 parameter in all 3 lines of annovar_annotation.pl file and again did database annotation and now its running fine . Also check whether your annotated vcf file is proper or not , like in my case one of the column name was '1' so i changed it to 'TUMOR' and its working now no errors. Hope it helps. Thanks

Hi I met the same error. But i use the test vcf in dir ISOWN/training_data/ and it was called in hg19. did you know the qpipeline_internal means? i met the error like no glibc-2.14, and do not run the qpipeline_internal strep where run database_annotation.pl Thanks

slavnycoder commented 4 years ago

try change /ISOWN/bin/annovar_annotation.pl:35 -buildver hg19 -> -buildver hg19_25

zjiang-lji commented 3 years ago

@itamuria, have you received any solution from the authors?

zjiang-lji commented 3 years ago

@slavnycoder, I changed -buildver hg19 to -buildver hg19_25 in /ISOWN/bin/annovar_annotation.pl:35. Then I was prompted to do the following but no commands are working:

The gene annotation database <redacted>/ISOWN/bin/../external_tools/annovar/humandb/hg19_25_refGene.txt does not exist.
Please use 'annotate_variation.pl --downdb refGene <redacted>/ISOWN/bin/../external_tools/annovar/humandb -build hg19_25' to download the database.

How were you able to annotate with Annovar hg19_25 using

perl $cwd/../external_tools/annovar/annotate_variation.pl -geneanno ${outputVCFFile}.temp.convert2annovar -buildver hg19_25 $cwd/../external_tools/annovar/humandb`

in /ISOWN/bin/annovar_annotation.pl?