Issues generating the annotated.eff.vcf file : Sanity check his should never happen
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11 months ago
cae453 • 0

Hello,

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! at org.snpeff.interval.Gene.circularClone(Gene.java:195) at org.snpeff.interval.Genes.createCircularGenes(Genes.java:53) at org.snpeff.snpEffect.SnpEffectPredictor.buildForest(SnpEffectPredictor.java:146) at org.snpeff.SnpEff.loadDb(SnpEff.java:617) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:940) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:923) at org.snpeff.SnpEff.run(SnpEff.java:1188) at org.snpeff.SnpEff.main(SnpEff.java:168)

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

-----------------------------------------------

Genome name : 'Arabidopsis_thaliana'

Genome version : 'Tair10.1'

Genome ID : 'Tair10.1[0]'

Has protein coding info : true

Has Tr. Support Level info : true

Genes : 38311

Protein coding genes : 27444

-----------------------------------------------

Transcripts : 59994

Avg. transcripts per gene : 1.57

TSL transcripts : 0

-----------------------------------------------

Checked transcripts :

AA sequences : 0 ( 0.00% )

DNA sequences : 0 ( 0.00% )

-----------------------------------------------

Protein coding transcripts : 48147

Length errors : 35 ( 0.07% )

STOP codons in CDS errors : 33 ( 0.07% )

START codon errors : 63 ( 0.13% )

STOP codon warnings : 38 ( 0.08% )

UTR sequences : 44634 ( 74.40% )

Total Errors : 100 ( 0.21% )

-----------------------------------------------

Cds : 286237

Exons : 324728

Exons with sequence : 324728

Exons without sequence : 0

Avg. exons per transcript : 5.41

WARNING : No mitochondrion chromosome found

-----------------------------------------------

Number of chromosomes : 7

Chromosomes : Format 'chromo_name size codon_table'

'NC_003070.9' 30427671 Standard

'NC_003076.8' 26975502 Standard

'NC_003074.8' 23459830 Standard

'NC_003071.7' 19698289 Standard

'NC_003075.7' 18585056 Standard

'NC_037304.1' 367808 Standard

'NC_000932.1' 154478 Standard

-----------------------------------------------

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.

Thank you!

Carlos Erazo

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