Much fewer than expected exons.

[EvanKomp]

Hello! Thanks for any assistance in advance. I am trying to generate a genome for C. necator. I have tried both genomes here. The resulting GTF files have the expected ~6,000 genes. When I run the genomeGenerate protocol I get 80 exons.

Here is the run command:
STAR --runThreadN 4 --runMode genomeGenerate --genomeDir $(pwd) --genomeFastaFiles GCA_004798725.1_ASM479872v1_genomic.fna --sjdbGTFfile genomic.gtf --sjdbOverhang 150 --genomeSAindexNbases 5 --sjdbGTFfeatureExon exon

And the head of the input files:

>chr1 Cupriavidus necator H16 chromosome 1, complete sequence
TCTGTCTTGCTGCCGGCCGTGTTTATGCATGTGCAGGTCGCTAACCTGTTAGCAAGGACGGCACGAACAGGCCAGACCCG
GCGATGCGCATACGTGATCCCCTGCCGCATCGCAGAACCCGGCATTTAACCGATTTTCTGCGGCAATGTCAAGGCGCAAG
ACTATGTGCACCGGCACAATTGCCACACCCGTCTGTGGCCCGTGGTGCGCCATTGTCCACAAAGGCCAGTGGGTAACTGC
AAGTGTCCCGAGGGCCACCTCTACCGCATCCATCCACAGGCGAAGTCCCTGTTTTGCCTGAGATTTCCCCCGTTTCCACA
CCCCGGAAAGCCGCATCGCACCAAGGGTTGTGCACACAAATCCACTGCATTTGCACAAGTTATCCACAGACTTATCCTTT
GTGGATAACTCAGGGGCGGGGGTACAATCCGGGTCCAAACACAACACGGGCTGCGTGGCGCAGGCGCAACCCGGGCCCCC
ACCGCGGCAACGCATGACTGAACGCACGCCAGTGCGGCGAGCCTGAAGGCTCGCTTGCTGCTGCATTGGCATGCCGCGGA
GGCCTCACCGAACGGAATTGATTCCTAATACGGTAAGGATGGCCCGGATCGCGCGGCGTAGATGCTGCTTGTGGCGTGCC
GGGGGAACCGCTGATTTGCGGCCGGGTACGATTACCAAAAAACAAACAATGCAAGATTTCTGGCAGGCGGCAGCAGCGCA

#gtf-version 2.2
#!genome-build ASM479872v1
#!genome-build-accession NCBI_Assembly:GCA_004798725.1
#!annotation-date 04/11/2019 14:49:50
#!annotation-source NCBI 
chr1    Genbank gene    689     2455    .       +       .       gene_id "E6A55_00005"; transcript_id ""; gbkey "Gene"; gene "dnaA"; gene_biotype "protein_coding"; locus_tag "E6A55_00005"; 
chr1    Protein Homology        CDS     689     2452    .       +       0       gene_id "E6A55_00005"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "dnaA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_011614275.1"; locus_tag "E6A55_00005"; product "chromosomal replication initiator protein DnaA"; protein_id "QCB99128.1"; transl_table "11"; exon_number "1"; 
chr1    Protein Homology        start_codon     689     691     .       +       0       gene_id "E6A55_00005"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "dnaA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_011614275.1"; locus_tag "E6A55_00005"; product "chromosomal replication initiator protein DnaA"; protein_id "QCB99128.1"; transl_table "11"; exon_number "1"; 
chr1    Protein Homology        stop_codon      2453    2455    .       +       0       gene_id "E6A55_00005"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "dnaA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_011614275.1"; locus_tag "E6A55_00005"; product "chromosomal replication initiator protein DnaA"; protein_id "QCB99128.1"; transl_table "11"; exon_number "1"; 
chr1    Genbank gene    2823    3938    .       +       .       gene_id "E6A55_00010"; transcript_id ""; gbkey "Gene"; gene_biotype "protein_coding"; locus_tag "E6A55_00010"; 

Here is the log:|

STAR version=2.7.5a
STAR compilation time,server,dir=Tue Jun 16 16:47:12 GMT 2020 :/Users/travis/build/alexdobin/travis-tests/STARcompile/source
##### Command Line:
STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /Users/ekomp/Documents/repos/RNA-seq/data/genome --genomeFastaFiles GCA_004798725.1_ASM479872v1_genomic.fna --sjdbGTFfile genomic.gtf --sjdbOverhang 150 --genomeSAindexNbases 5 --sjdbGTFfeatureExon exon
##### Initial USER parameters from Command Line:
###### All USER parameters from Command Line:
runThreadN                    4     ~RE-DEFINED
runMode                       genomeGenerate     ~RE-DEFINED
genomeDir                     /Users/ekomp/Documents/repos/RNA-seq/data/genome     ~RE-DEFINED
genomeFastaFiles              GCA_004798725.1_ASM479872v1_genomic.fna        ~RE-DEFINED
sjdbGTFfile                   genomic.gtf     ~RE-DEFINED
sjdbOverhang                  150     ~RE-DEFINED
genomeSAindexNbases           5     ~RE-DEFINED
sjdbGTFfeatureExon            exon     ~RE-DEFINED
##### Finished reading parameters from all sources

##### Final user re-defined parameters-----------------:
runMode                           genomeGenerate
runThreadN                        4
genomeDir                         /Users/ekomp/Documents/repos/RNA-seq/data/genome
genomeFastaFiles                  GCA_004798725.1_ASM479872v1_genomic.fna   
genomeSAindexNbases               5
sjdbGTFfile                       genomic.gtf
sjdbGTFfeatureExon                exon
sjdbOverhang                      150

-------------------------------
##### Final effective command line:
STAR   --runMode genomeGenerate   --runThreadN 4   --genomeDir /Users/ekomp/Documents/repos/RNA-seq/data/genome   --genomeFastaFiles GCA_004798725.1_ASM479872v1_genomic.fna      --genomeSAindexNbases 5   --sjdbGTFfile genomic.gtf   --sjdbGTFfeatureExon exon   --sjdbOverhang 150
----------------------------------------

Number of fastq files for each mate = 1
Finished loading and checking parameters
--genomeDir directory exists and will be overwritten: /Users/ekomp/Documents/repos/RNA-seq/data/genome/
Sep 30 14:03:07 ... starting to generate Genome files
GCA_004798725.1_ASM479872v1_genomic.fna : chr # 0  "chr1" chrStart: 0
GCA_004798725.1_ASM479872v1_genomic.fna : chr # 1  "chr2" chrStart: 4194304
GCA_004798725.1_ASM479872v1_genomic.fna : chr # 2  "chr3" chrStart: 7340032
Sep 30 14:03:07 ..... processing annotations GTF
Processing pGe.sjdbGTFfile=genomic.gtf, found:
		83 transcripts
		83 exons (non-collapsed)
		0 collapsed junctions
Total junctions: 0
Sep 30 14:03:07 ..... finished GTF processing

Estimated genome size=308864320 = 7864320 + 301000000
GstrandBit=32
Number of SA indices: 14829122
Sep 30 14:03:07 ... starting to sort Suffix Array. This may take a long time...
Number of chunks: 4;   chunks size limit: 39544320 bytes
Sep 30 14:03:07 ... sorting Suffix Array chunks and saving them to disk...
Writing 1639784 bytes into /Users/ekomp/Documents/repos/RNA-seq/data/genome//SA_3 ; empty space on disk = 371697975820288 bytes ... done
Writing 39011608 bytes into /Users/ekomp/Documents/repos/RNA-seq/data/genome//SA_0 ; empty space on disk = 371697555341312 bytes ... done
Writing 38527992 bytes into /Users/ekomp/Documents/repos/RNA-seq/data/genome//SA_1 ; empty space on disk = 371687567654912 bytes ... done
Writing 39453592 bytes into /Users/ekomp/Documents/repos/RNA-seq/data/genome//SA_2 ; empty space on disk = 371677703700480 bytes ... done
Sep 30 14:03:08 ... loading chunks from disk, packing SA...
Sep 30 14:03:08 ... finished generating suffix array
Sep 30 14:03:08 ... generating Suffix Array index
Sep 30 14:03:08 ... completed Suffix Array index
Sep 30 14:03:08   Finished preparing junctions
Sep 30 14:03:08 ..... finished inserting junctions into genome
Sep 30 14:03:08 ... writing Genome to disk ...
Writing 7864320 bytes into /Users/ekomp/Documents/repos/RNA-seq/data/genome//Genome ; empty space on disk = 371699988037632 bytes ... done
SA size in bytes: 61170132
Sep 30 14:03:08 ... writing Suffix Array to disk ...
Writing 61170132 bytes into /Users/ekomp/Documents/repos/RNA-seq/data/genome//SA ; empty space on disk = 371713635254272 bytes ... done
Sep 30 14:03:08 ... writing SAindex to disk
Writing 8 bytes into /Users/ekomp/Documents/repos/RNA-seq/data/genome//SAindex ; empty space on disk = 371697976868864 bytes ... done
Writing 48 bytes into /Users/ekomp/Documents/repos/RNA-seq/data/genome//SAindex ; empty space on disk = 371697976868864 bytes ... done
Writing 5971 bytes into /Users/ekomp/Documents/repos/RNA-seq/data/genome//SAindex ; empty space on disk = 371697976868864 bytes ... done
Sep 30 14:03:08 ..... finished successfully
DONE: Genome generation, EXITING

I have beat my head against a couple of parameters and cannot get the genome to come out with more that ~80 transcripts. Thanks for your time.