SNPEFF genome build with specific codon usage 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.&lt;init&gt;(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

&gt;1 dna:chromosome chromosome:TAIR10:1:1:30427671:1 REF
&gt;2 dna:chromosome chromosome:TAIR10:2:1:19698289:1 REF
&gt;3 dna:chromosome chromosome:TAIR10:3:1:23459830:1 REF
&gt;4 dna:chromosome chromosome:TAIR10:4:1:18585056:1 REF
&gt;5 dna:chromosome chromosome:TAIR10:5:1:26975502:1 REF
&gt;Mt dna:chromosome chromosome:TAIR10:Mt:1:366924:1 REF
&gt;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
codon table issue

I solved the issue with codon tables, the correct way to specify a table is the following:

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


Note that one should remove the leading prefix 'codon.' from the name of the tables chosen from the config file

Concerning accessory files:

data to reproduce this issue:

baseurl="ftp://ftp.ensemblgenomes.org/pub/plants/release-46"
wget ${baseurl}/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz
wget ${baseurl}/fasta/arabidopsis_thaliana/cds/Arabidopsis_thaliana.TAIR10.cds.all.fa.gz
wget ${baseurl}/fasta/arabidopsis_thaliana/pep/Arabidopsis_thaliana.TAIR10.pep.all.fa.gz
wget ${baseurl}/gff3/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.46.gff3.gz
wget ${baseurl}/variation/vcf/arabidopsis_thaliana/arabidopsis_thaliana_incl_consequences.vcf.gz


I suspect that the format used by Ensembl is not 100% OK for SnpEff; I therefore simplified the fasta headers to keep only the first argument (name) and remove the remaining of the line

eg.

&gt;AT3G05780.1 pep chromosome:TAIR10:3:1714941:1719608:-1 gene:AT3G05780 transcript:AT3G05780.1 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:LON3 description:Lon protease homolog 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M9L8]


becomes

&gt;AT3G05780.1


Despite this modification, I still have an issue with

java -jar /opt/biotools/snpEff/SnpEff.jar build -gff3 -v Arabidopsis_thaliana_TAIR10_46 2&gt;&amp;1 | tee -a log.txt



a LOT of warning about not being able to add UTR while it seems that UTR's are well present in the GFF3 file



  Reading GFF3 data file  :
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  WARNING: Cannot find transcript 'transcript:AT1G01010.1'. File
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  line
  18    '1  araport11   five_prime_UTR  3631    3759    .   +   .   Parent=transcript:AT1G01010.1'
  WARNING: Could not add UTR. File
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  line
  18    '1  araport11   five_prime_UTR  3631    3759    .   +   .   Parent=transcript:AT1G01010.1'
  WARNING: Cannot find transcript 'transcript:AT1G01020.3'. File
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  line
  69    '1  araport11   three_prime_UTR 6788    6914    .   -   .   Parent=transcript:AT1G01020.3'
  WARNING: Could not add UTR. File
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  line
  69    '1  araport11   three_prime_UTR 6788    6914    .   -   .   Parent=transcript:AT1G01020.3'
  WARNING: Cannot find transcript 'transcript:AT1G01020.5'. File
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  line
  88    '1  araport11   three_prime_UTR 6788    6914    .   -   .   Parent=transcript:AT1G01020.5'
  WARNING: Could not add UTR. File
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  line
  88    '1  araport11   three_prime_UTR 6788    6914    .   -   .   Parent=transcript:AT1G01020.5'
  WARNING: Cannot find transcript 'transcript:AT1G01020.4'. File
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  line
  109   '1  araport11   three_prime_UTR 6788    6914    .   -   .   Parent=transcript:AT1G01020.4'
  WARNING: Could not add UTR. File
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  line
  109   '1  araport11   three_prime_UTR 6788    6914    .   -   .   Parent=transcript:AT1G01020.4'
  WARNING: Cannot find transcript 'transcript:AT1G01020.1'. File
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  line
  128   '1  araport11   three_prime_UTR 6788    6914    .   -   .   Parent=transcript:AT1G01020.1'
  WARNING: Could not add UTR. File
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  line
  128   '1  araport11   three_prime_UTR 6788    6914    .   -   .   Parent=transcript:AT1G01020.1'
  WARNING: Cannot find transcript 'transcript:AT1G01030.1'. File
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/genes.gff'
  line 155  '1  araport11   three_prime_UTR 11649   11863   .   -   .   Parent



nothing good coming out of the cds.fa input although I treated it with the same name fix as the pep file



  00:00:19  CDS check (FASTA file):
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/cds.fa'
  
  00:00:19  Checking database using CDS sequences 00:00:19  Reading CDSs
  from file
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/cds.fa'...
  00:00:20  done (75976 CDSs). 00:00:20 Comparing CDS...    Labels:         '+' :
  OK        '.' : Missing       '*' : Error
    ....................................................................................................
    ....................................................................................................
    ....................................................................................................
  
  many more lines with dots
    ....................................................................................................
    ....................................................................................................
    ....................................................................................................
    ...............................     CDS
  check:    Arabidopsis_thaliana_TAIR10_46  OK: 0   Warnings: 0 Not found:
  104147    Errors: 0   Error percentage: NaN% Fatal error: No CDS checked.
  This is might be caused by differences in FASTA file transcript IDs
  respect to database's transcript's IDs. Transcript IDs from database
  (sample):     'transcript:AT3G12250.7'    'transcript:AT5G18570.1'
    'AT3G27810.1'   'AT3G27810.2'   'transcript:AT2G16810.1'
    'transcript:AT3G01170.1'    'AT4G37030.1'   'transcript:AT1G79940.4'
    'transcript:AT2G44850.1'    'AT1G49540.1'   'AT1G49540.2'
    'transcript:AT4G35290.5'    'transcript:AT4G15840.2'
    'transcript:AT4G27500.1'    'AT4G37022.1'   'transcript:AT2G40008.1'
    'AT3G27820.1'   'transcript:AT4G24265.1'    'transcript:AT2G20618.1'
    'transcript:AT4G18375.2'    'AT4G37020.2'   'AT4G37020.1' Transcript IDs
  from database (fasta file):   'AT4G02541'     'AT1G12410.1'   'AT4G26510'
    'AT4G02540'     'AT3G04500.1'   'AT3G04500.2'   'AT3G04500.3'   'AT2G36250'
    'AT5G63350'     'AT2G36255'     'AT2G12280'     'AT1G03970.1'   'AT5G18390.1'
    'AT3G04490.4'   'AT5G38386'     'AT3G04490.2'   'AT3G04490.3'
    'AT3G04490.1'   'AT5G38380'     'AT4G02530'     'AT4G26520'     'AT1G69280.2'


link to the full stdout log after running the command without cds.fa

https://www.dropbox.com/s/gxa4e533p64wxm9/SnpEff_build-log.txt?dl=1