SNPEFF genome build with specific codon usage
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17 months ago

Failing to build my own Arabidopsis thaliana reference with Mt using 'codon.Mitochondrial' and Pt using 'codon.Bacterial_and_Plant_Plastid' but the same commands works well with both lines with codon tables removed below.

The snpeff commands

java -Xms24g -Xmx24g -jar /opt/biotools/snpEff/snpEff.jar build -gff3 -v Arabidopsis_thaliana.TAIR10.46

returns:

java.lang.RuntimeException: Error parsing property 'Arabidopsis_thaliana.TAIR10.46.Pt.codonTable'. No such codon table 'codon.Bacterial_and_Plant_Plastid'
        at org.snpeff.snpEffect.Config.createCodonTables(Config.java:169)
        at org.snpeff.snpEffect.Config.readConfig(Config.java:650)
        at org.snpeff.snpEffect.Config.init(Config.java:480)
        at org.snpeff.snpEffect.Config.<init>(Config.java:117)
        at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
        at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1000)
        at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
        at org.snpeff.SnpEff.run(SnpEff.java:1183)
        at org.snpeff.SnpEff.main(SnpEff.java:162)

(same error for the Mt when removing Pt)

my fasta has the two chromosomes

>1 dna:chromosome chromosome:TAIR10:1:1:30427671:1 REF
>2 dna:chromosome chromosome:TAIR10:2:1:19698289:1 REF
>3 dna:chromosome chromosome:TAIR10:3:1:23459830:1 REF
>4 dna:chromosome chromosome:TAIR10:4:1:18585056:1 REF
>5 dna:chromosome chromosome:TAIR10:5:1:26975502:1 REF
>Mt dna:chromosome chromosome:TAIR10:Mt:1:366924:1 REF
>Pt dna:chromosome chromosome:TAIR10:Pt:1:154478:1 REF

my data folder is OK

data/Arabidopsis_thaliana.TAIR10.46/
drwxr-xr-x   3 u0002316 domain users 4.0K Apr 15 13:33 .
drwxr-xr-x 244 u0002316 domain users  16K Apr 10 09:39 ..
-rw-r--r--   1 u0002316 domain users 106M Apr 10 09:40 genes.gff
-rw-r--r--   1 u0002316 domain users 117M Apr 10 09:40 sequences.fa

my snpeff.config contains:

Arabidopsis_thaliana.TAIR10.46.genome : Arabidopsis_thaliana.TAIR10.46
Arabidopsis_thaliana.TAIR10.46.Mt.codonTable : codon.Mitochondrial
Arabidopsis_thaliana.TAIR10.46.Pt.codonTable : codon.Bacterial_and_Plant_Plastid

the two codon tables are present by default in the snpeff.config

codon.Mitochondrial                         : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G

codon.Bacterial_and_Plant_Plastid           : TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G

Anybody ever succeeded to build a custom genome with specific codon tables?

Thanks in advance

SnpEff variants annotation • 533 views
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