Error when running SNPEff
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0
Entering edit mode
4.5 years ago
l0o0 ▴ 210

I want to anntate SNP in vcf format generated by GATK. Reference fasta and gff files were downloaded from http://www.phytozome.net/, Citrus clementina.

Make directory data/cle and data/genomes, bash data ├── cle │   ├── genes.gff └── genomes └── cle.fa

Adding reference information in snpEFF.config:

#Cclementina, version Citrus clementina
cle.genome : Cclementina

Build database manually by running:
bash java -jar snpEff.jar build -gff3 -v cle

After that run:
bash java -Xmx4g -jar snpEff.jar -ud 1000 cle file.vcf > new.file.vcf then there comes an error:

Error: Error while processing VCF entry (line 1514) :
scaffold_1 68760 . CAT C 37.73 QD AC=1;AF=0.500;AN=2;BaseQRankSum=-0.852;ClippingRankSum=-1.445;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.00;MQRankSum=0.556;QD=1.51;ReadPosRankSum=0.630;SOR=0.465;ANN=C|downstream_gene_variant|MODIFIER|Ciclev10009318m.g|Ciclev10009318m.g.v1.0|transcript|Ciclev10009781m.v1.0|protein_coding||c.1407_1408delAT|||||122|WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|Ciclev10009318m.g|Ciclev10009318m.g.v1.0|transcript|Ciclev10009318m.v1.0|protein_coding|4/6|c.481+28_481+29delAT||||||,C|intron_variant|MODIFIER|Ciclev10009318m.g|Ciclev10009318m.g.v1.0|transcript|Ciclev10009356m.v1.0|protein_coding|4/6|c.481+28_481+29delAT||||||,C|intron_variant|MODIFIER|Ciclev10009318m.g|Ciclev10009318m.g.v1.0|transcript|Ciclev10009638m.v1.0|protein_coding|1/3|c.0-411_0-410delAT||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|Ciclev10009318m.g|Ciclev10009318m.g.v1.0|transcript|Ciclev10009675m.v1.0|protein_coding|1/3|c.0-23_0-22delAT||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|Ciclev10009318m.g|Ciclev10009318m.g.v1.0|transcript|Ciclev10009637m.v1.0|protein_coding|1/3|c.0-411_0-410delAT||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|Ciclev10009318m.g|Ciclev10009318m.g.v1.0|transcript|Ciclev10009674m.v1.0|protein_coding|1/3|c.0-23_0-22delAT||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|Ciclev10009318m.g|Ciclev10009318m.g.v1.0|transcript|Ciclev10009683m.v1.0|protein_coding|1/2|c.0-672_0-671delAT||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:DP:GQ:PL 0/1:21,4:25:75:75,0,910 java.lang.RuntimeException: Interval error: end before start.
Class : Marker
Start : 68241
End : 67353
ID :
Parent class : Chromosome
Parent : scaffold_1 0-28940637 CHROMOSOME 'scaffold_1'
java.lang.RuntimeException: Interval error: end before start.
Class : Marker
Start : 68241
End : 67353
ID :
Parent class : Chromosome
Parent : scaffold_1 0-28940637 CHROMOSOME 'scaffold_1'
at ca.mcgill.mcb.pcingola.interval.Interval.<init>(Interval.java:38)
at ca.mcgill.mcb.pcingola.interval.Marker.<init>(Marker.java:37)
at ca.mcgill.mcb.pcingola.snpEffect.LossOfFunction.isLofDeletion(LossOfFunction.java:226)
at ca.mcgill.mcb.pcingola.snpEffect.LossOfFunction.isLof(LossOfFunction.java:155)
at ca.mcgill.mcb.pcingola.snpEffect.LossOfFunction.isLof(LossOfFunction.java:115)
at ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.addInfo(VcfOutputFormatter.java:170)
at ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.toString(VcfOutputFormatter.java:285)
at ca.mcgill.mcb.pcingola.outputFormatter.OutputFormatter.endSection(OutputFormatter.java:112)
at ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.endSection(VcfOutputFormatter.java:229)
at ca.mcgill.mcb.pcingola.outputFormatter.OutputFormatter.printSection(OutputFormatter.java:145)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:278)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:446)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:138)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:939)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:978)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:136)

Line 1514 of vcf is :

scaffold_1 68760 . CAT C 37.73 QD AC=1;AF=0.500;AN=2;BaseQRankSum=-0.852;ClippingRankSum=-1.445;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.00;MQRankSum=0.556;QD=1.51;ReadPosRankSum=0.630;SOR=0.465 GT:AD:DP:GQ:PL 0/1:21,4:25:75:75,0,910

The snpEFF version i use is SnpEff 4.2. Any help will be appreciated.

SNP SNPEFF • 2.2k views
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0
Entering edit mode
4.5 years ago

In your long error message there is

java.lang.RuntimeException: Interval error: end before start.
Class : Marker Start : 68241 End : 67353.

My guess is that something is wrong with your annotation. Try searching in the gff file for position 68241 or 67353 and see if indeed there is an end position before the start.

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0
Entering edit mode

The gff seems ok, I fixed this error by using version 4.1l. It's a strange error.

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