how to build a .gtf for simple ATG-to-stop codon CDS references

I followed the instructions on how to build a .gtf file, for a simple use case where we have a CDS without introns from the ATG-to-the-stop codon.

When I create it in this manner:

cat Khanna_j4h_8_DMX8/genes.gtf | tabtk view
Khanna_j4h_8_DMX8       ensembl gene            1       1340    .       +       .       gene_id "Khanna_j4h_8_DMX8.1"; gene_type "protein_coding";
Khanna_j4h_8_DMX8       ensembl transcript      1       1337    .       +       .       parent "Khanna_j4h_8_DMX8.1"; gene_id "Khanna_j4h_8_DMX8.1"; transcript_id "Khanna_j4h_8_DMX8.2"; transcript_type "protein_coding";
Khanna_j4h_8_DMX8       ensembl exon            1       1337    .       +       .       transcript_id "Khanna_j4h_8_DMX8.2";
Khanna_j4h_8_DMX8       ensembl CDS             1       1337    .       +       0       transcript_id "Khanna_j4h_8_DMX8.2";

I get the following report from running the build command:

java -jar ~/snpEff/snpEff.jar build -gtf22 -v Khanna_j4h_8_DMX8

00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'          
00:00:00 Building database for 'Khanna_j4h_8_DMX8'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Khanna_j4h_8_DMX8'
00:00:00 Reading config file: /home/penguin/snpEff/data/snpEff.config
00:00:00 Reading config file: /home/penguin/snpEff/snpEff.config
00:00:00 done
00:00:00 Reading GTF22 data file  : '/home/penguin/snpEff/./data/Khanna_j4h_8_DMX8/genes.gtf'
00:00:00 Reading file '/home/penguin/snpEff/./data/Khanna_j4h_8_DMX8/genes.gtf'
00:00:00 
        Total: 3 markers added.
00:00:00 Create exons from CDS (if needed): 
00:00:00 Exons created for 0 transcripts.
00:00:00 Deleting redundant exons (if needed): 
00:00:00        Total transcripts with deleted exons: 0
00:00:00 Collapsing zero length introns (if needed):  
00:00:00        Total collapsed transcripts: 0
00:00:00        Reading sequences   :
00:00:00        FASTA file: '/home/penguin/snpEff/./data/genomes/Khanna_j4h_8_DMX8.fa' not found.
00:00:00        Reading FASTA file: '/home/penguin/snpEff/./data/Khanna_j4h_8_DMX8/sequences.fa'
00:00:00                Reading sequence 'Khanna_j4h_8_DMX8', length: 1340
00:00:00                Adding genomic sequences to genes: 
00:00:00        Done (1 sequences added).
00:00:00                Adding genomic sequences to exons: 
00:00:00        Done (1 sequences added, 0 ignored).
00:00:00        Total: 1 sequences added, 0 sequences ignored.
00:00:00 Finishing up genome
00:00:00 Adjusting transcripts: 
00:00:00 Adjusting genes: 
WARNING_GENE_COORDINATES: Gene 'Khanna_j4h_8_DMX8.1' (name:'Khanna_j4h_8_DMX8.1'), adjusting end coordinate from 1339 to 1336
00:00:00 Adjusting chromosomes lengths: 
00:00:00 Ranking exons: 
00:00:00 Create UTRs from CDS (if needed):                                                                                                                                                                [12/1932]
00:00:00 Correcting exons based on frame information.

00:00:00 
00:00:00 Remove empty chromosomes: 
00:00:00 Marking as 'coding' from CDS information: 
00:00:00 Done: 0 transcripts marked
00:00:00 
00:00:00 #-----------------------------------------------
# Genome name                : 'Khanna_j4h_8_DMX8'
# Genome version             : 'Khanna_j4h_8_DMX8'
# Genome ID                  : 'Khanna_j4h_8_DMX8[0]'
# Has protein coding info    : true
# Has Tr. Support Level info : true
# Genes                      : 1
# Protein coding genes       : 1
#-----------------------------------------------
# Transcripts                : 1
# Avg. transcripts per gene  : 1.00
# TSL transcripts            : 0
#-----------------------------------------------
# Checked transcripts        : 
#               AA sequences :      0 ( 0.00% )
#              DNA sequences :      0 ( 0.00% )
#-----------------------------------------------
# Protein coding transcripts : 1
#              Length errors :      1 ( 100.00% )
#  STOP codons in CDS errors :      0 ( 0.00% )
#         START codon errors :      0 ( 0.00% )
#        STOP codon warnings :      0 ( 0.00% )
#              UTR sequences :      0 ( 0.00% )
#               Total Errors :      1 ( 100.00% )
# WARNING                    : No protein coding transcript has UTR
#-----------------------------------------------
# Cds                        : 1
# Exons                      : 1
# Exons with sequence        : 1
# Exons without sequence     : 0
# Avg. exons per transcript  : 1.00
#-----------------------------------------------
# Number of chromosomes      : 1
# Chromosomes                : Format 'chromo_name size codon_table'
#               'Khanna_j4h_8_DMX8'     1340    Standard
#-----------------------------------------------

00:00:00 Caracterizing exons by splicing (stage 1) :  
00:00:00 Caracterizing exons by splicing (stage 2) :  
        00:00:00 done.          
00:00:00 [Optional] Rare amino acid annotations
WARNING_FILE_NOT_FOUND: Rare Amino Acid analysis: Cannot read protein sequence file '/home/penguin/snpEff/./data/Khanna_j4h_8_DMX8/protein.fa', nothing done.
ERROR: CDS check file '/home/penguin/snpEff/./data/Khanna_j4h_8_DMX8/cds.fa' not found.
ERROR: Protein check file '/home/penguin/snpEff/./data/Khanna_j4h_8_DMX8/protein.fa' not found.
ERROR: Database check failed.                                                                            
00:00:00 Logging                                                                                         
00:00:01 Checking for updates...                
00:00:02 Done.

Any ideas where the issue could be? Do the reference sequences need to have a minimal UTR?

pcingola / SnpEff

how to build a .gtf for simple ATG-to-stop codon CDS references #500