Issues generating the annotated.eff.vcf file : Sanity check his should never happen
I am having a hard time deciphering the error associated with the vcf annotation file. I used the command: java -Xmx8g -jar snpEff.jar Tair10.1 /globalhome/cae453/HPC/sample6.vcf > /globalhome/cae453/HPC/sample6.eff.vcf
The output is
java.lang.RuntimeException: Sanity check: This should never happen!
In the end, the eff.vcf file is empty
Previously, to perform the annotation I had to build a genome database (Tair10.1) executing the following command:
Building database java -jar snpEff.jar build -gtf22 -v Tair10.1. The database doesn’t have errors apparently:
Remove empty chromosomes:
Marking as 'coding' from CDS information:
Done: 48147 transcripts marked
I also tried building the database using GFF.file but appears more warning messages and error in the built database associated with Start and Stop codon. Even though when I use this database to perform the vcf file annotation the file is not empty but has a lot of WARNING_TRANSCRIPT_NO_START_CODON.
At this moment I don’t know how to fix the error associated with the empty vcf. file I will really appreciate any help that you can provide me.