<p><strong>codon table issue</strong></p>

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

<pre><code>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
</code></pre>

<p><em>Note</em> that one should remove the leading prefix '<strong>codon.</strong>' from the name of the tables chosen from the config file</p>

<p><strong>Concerning accessory files:</strong></p>

<p>data to reproduce this issue:</p>

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

<p>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</p>

<p>eg.</p>

<pre><code>&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]
</code></pre>

<p>becomes</p>

<pre><code>&gt;AT3G05780.1
</code></pre>

<p><strong>Despite this modification, I still have an issue with</strong></p>

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

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

<blockquote>
  <p>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</p>
</blockquote>

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

<blockquote>
  <p>00:00:19  CDS check (FASTA file):
  '/opt/biotools/snpEff_v4.4/./data/Arabidopsis_thaliana_TAIR10_46/cds.fa'</p>
  
  <p>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
    ....................................................................................................
    ....................................................................................................
    ....................................................................................................</p>
  
  <p>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'</p>
</blockquote>

<p><strong>link to the full stdout log after running the command without cds.fa</strong></p>

<p><a href="https://www.dropbox.com/s/gxa4e533p64wxm9/SnpEff_build-log.txt?dl=1" rel="nofollow noreferrer">https://www.dropbox.com/s/gxa4e533p64wxm9/SnpEff_build-log.txt?dl=1</a></p>

CC BY-SA 4.0
2020-04-17T14:38:04.673Z
2020-04-17T14:38:04.673Z
splaisan
<p>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.</p>

<p>The snpeff commands </p>

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

<p>returns:</p>

<pre><code>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)
</code></pre>

<p>(same error for the Mt when removing Pt)</p>

<p>my fasta has the two chromosomes</p>

<pre><code>&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
</code></pre>

<p>my data folder is OK</p>

<pre><code>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
</code></pre>

<p>my snpeff.config contains:</p>

<pre><code>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
</code></pre>

<p>the two codon tables are present by default in the snpeff.config</p>

<pre><code>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
</code></pre>

<p>Anybody ever succeeded to build a custom genome with specific codon tables?</p>

<p>Thanks in advance</p>

<sequence-annotation><variants>
SNPEFF genome build with specific codon usage
# SNPEFF genome build with specific codon usage

(Asked by: username_0 on 2020-04-16)

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.(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

**Tags:** sequence-annotation, variants

---

## 1 answers

### Answer by username_0 on 2020-04-17. Score: 2

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.
>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
>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>&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


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