ValueError: Can't transform the genomic interval, please check!

[koosle]

Dear author,
I met a problem with that,

 Preparing annotation files ...
        Process the transcripts ....
        Reading the GTF file: E.coli.gtf .......
Traceback (most recent call last):
  File "/home/jinwen/miniconda3/bin/prepare_transcripts", line 10, in <module>
    sys.exit(main())
  File "/home/jinwen/miniconda3/lib/python3.6/site-packages/RiboCode/prepare_transcripts.py", line 388, in main
    processTranscripts(args.genomeFasta,args.gtfFile,args.out_dir)
  File "/home/jinwen/miniconda3/lib/python3.6/site-packages/RiboCode/prepare_transcripts.py", line 354, in processTranscripts
    tobj.stopcodon = genomic_iv_transform(tobj.genomic_exons,tobj.genomic_stopcodon)
  File "/home/jinwen/miniconda3/lib/python3.6/site-packages/RiboCode/prepare_transcripts.py", line 232, in genomic_iv_transform
    raise ValueError("\tCan't transform the genomic interval, please check!")
ValueError:     Can't transform the genomic interval, please check!

Could you help me to check my gtf files?

NZ_CP053601.1	RefSeq	gene	499400	499573	.	+	.	gene_id "HO397_RS02325"; transcript_id ""; gbkey "Gene"; gene_biotype "protein_coding"; locus_tag "HO397_RS02325"; old_locus_tag "HO397_02325"; transcript_biotype "protein_coding";
NZ_CP053601.1	RefSeq	transcript	499400	499573	.	+	.	gene_id "HO397_RS02325"; transcript_id "unassigned_transcript_472"; gbkey "Gene"; gene_biotype "protein_coding"; locus_tag "HO397_RS02325"; old_locus_tag "HO397_02325"; transcript_biotype "protein_coding";
NZ_CP053601.1	Protein Homology	CDS	499400	499570	.	+	0	gene_id "HO397_RS02325"; transcript_id "unassigned_transcript_472"; gbkey "CDS"; gene_biotype "protein_coding"; locus_tag "HO397_RS02325"; db_xref "GenBank:WP_001297301.1"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_001297301.1"; product "hypothetical protein"; protein_id "WP_001297301.1"; transl_table "11"; exon_number "1"; transcript_biotype "protein_coding";
NZ_CP053601.1	Protein Homology	exon	499400	499570	.	+	0	gene_id "HO397_RS02325"; transcript_id "unassigned_transcript_472"; gbkey "CDS"; gene_biotype "protein_coding"; locus_tag "HO397_RS02325"; db_xref "GenBank:WP_001297301.1"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_001297301.1"; product "hypothetical protein"; protein_id "WP_001297301.1"; transl_table "11"; exon_number "1"; transcript_biotype "protein_coding";
NZ_CP053601.1	Protein Homology	start_codon	499400	499402	.	+	0	gene_id "HO397_RS02325"; transcript_id "unassigned_transcript_472"; gbkey "CDS"; gene_biotype "protein_coding"; locus_tag "HO397_RS02325"; db_xref "GenBank:WP_001297301.1"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_001297301.1"; product "hypothetical protein"; protein_id "WP_001297301.1"; transl_table "11"; exon_number "1"; transcript_biotype "protein_coding";
NZ_CP053601.1	Protein Homology	stop_codon	499571	499573	.	+	0	gene_id "HO397_RS02325"; transcript_id "unassigned_transcript_472"; gbkey "CDS"; gene_biotype "protein_coding"; locus_tag "HO397_RS02325"; db_xref "GenBank:WP_001297301.1"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_001297301.1"; product "hypothetical protein"; protein_id "WP_001297301.1"; transl_table "11"; exon_number "1"; transcript_biotype "protein_coding";
NZ_CP053601.1	RefSeq	gene	500093	500458	.	-	.	gene_id "HO397_RS02330"; transcript_id ""; gbkey "Gene"; gene "ylbG"; gene_biotype "pseudogene"; locus_tag "HO397_RS02330"; old_locus_tag "HO397_02330"; partial "true"; pseudo "true"; transcript_biotype "pseudogene";
NZ_CP053601.1	RefSeq	transcript	500093	500458	.	-	.	gene_id "HO397_RS02330"; transcript_id "unassigned_transcript_473"; gbkey "Gene"; gene "ylbG"; gene_biotype "pseudogene"; locus_tag "HO397_RS02330"; old_locus_tag "HO397_02330"; partial "true"; pseudo "true"; transcript_biotype "pseudogene";
NZ_CP053601.1	Protein Homology	CDS	500096	500458	.	-	0	gene_id "HO397_RS02330"; transcript_id "unassigned_transcript_473"; gbkey "CDS"; gene "ylbG"; gene_biotype "pseudogene"; locus_tag "HO397_RS02330"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_014543172.1"; product "helix-turn-helix domain-containing protein"; transl_table "11"; exon_number "1"; partial "true"; pseudo "true"; note "incomplete; partial in the middle of a contig; missing C-terminus"; transcript_biotype "pseudogene";
NZ_CP053601.1	Protein Homology	exon	500096	500458	.	-	0	gene_id "HO397_RS02330"; transcript_id "unassigned_transcript_473"; gbkey "CDS"; gene "ylbG"; gene_biotype "pseudogene"; locus_tag "HO397_RS02330"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_014543172.1"; product "helix-turn-helix domain-containing protein"; transl_table "11"; exon_number "1"; partial "true"; pseudo "true"; note "incomplete; partial in the middle of a contig; missing C-terminus"; transcript_biotype "pseudogene";
NZ_CP053601.1	Protein Homology	start_codon	500456	500458	.	-	0	gene_id "HO397_RS02330"; transcript_id "unassigned_transcript_473"; gbkey "CDS"; gene "ylbG"; gene_biotype "pseudogene"; locus_tag "HO397_RS02330"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_014543172.1"; product "helix-turn-helix domain-containing protein"; transl_table "11"; exon_number "1"; partial "true"; pseudo "true"; note "incomplete; partial in the middle of a contig; missing C-terminus"; transcript_biotype "pseudogene";
NZ_CP053601.1	RefSeq	gene	446799	446895	.	+	.	gene_id "HO397_RS02095"; transcript_id ""; gbkey "Gene"; gene "ffs"; gene_biotype "SRP_RNA"; locus_tag "HO397_RS02095"; old_locus_tag "HO397_02095"; transcript_biotype "SRP_RNA";
NZ_CP053601.1	cmsearch	transcript	446799	446895	.	+	.	gene_id "HO397_RS02095"; transcript_id "unassigned_transcript_425"; gbkey "ncRNA"; gene "ffs"; gene_biotype "SRP_RNA"; locus_tag "HO397_RS02095"; db_xref "RFAM:RF00169"; inference "COORDINATES: profile:INFERNAL:1.1.5"; product "signal recognition particle sRNA small type"; transcript_biotype "SRP_RNA";
NZ_CP053601.1	cmsearch	exon	446799	446895	.	+	.	gene_id "HO397_RS02095"; transcript_id "unassigned_transcript_425"; gene "ffs"; gene_biotype "SRP_RNA"; locus_tag "HO397_RS02095"; db_xref "RFAM:RF00169"; inference "COORDINATES: profile:INFERNAL:1.1.5"; product "signal recognition particle sRNA small type"; exon_number "1"; transcript_biotype "SRP_RNA";
NZ_CP053601.1	RefSeq	gene	498395	499102	.	+	.	gene_id "HO397_RS02315"; transcript_id ""; gbkey "Gene"; gene_biotype "pseudogene"; locus_tag "HO397_RS02315"; old_locus_tag "HO397_02315"; partial "true"; pseudo "true"; transcript_biotype "pseudogene";
NZ_CP053601.1	RefSeq	transcript	498395	499102	.	+	.	gene_id "HO397_RS02315"; transcript_id "unassigned_transcript_470"; gbkey "Gene"; gene_biotype "pseudogene"; locus_tag "HO397_RS02315"; old_locus_tag "HO397_02315"; partial "true"; pseudo "true"; transcript_biotype "pseudogene";
NZ_CP053601.1	Protein Homology	CDS	498395	499099	.	+	0	gene_id "HO397_RS02315"; transcript_id "unassigned_transcript_470"; gbkey "CDS"; gene_biotype "pseudogene"; locus_tag "HO397_RS02315"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_308587.2"; product "RHS repeat-associated core domain-containing protein"; transl_table "11"; exon_number "1"; partial "true"; pseudo "true"; note "incomplete; partial in the middle of a contig; missing N-terminus"; transcript_biotype "pseudogene";
NZ_CP053601.1	Protein Homology	exon	498395	499099	.	+	0	gene_id "HO397_RS02315"; transcript_id "unassigned_transcript_470"; gbkey "CDS"; gene_biotype "pseudogene"; locus_tag "HO397_RS02315"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_308587.2"; product "RHS repeat-associated core domain-containing protein"; transl_table "11"; exon_number "1"; partial "true"; pseudo "true"; note "incomplete; partial in the middle of a contig; missing N-terminus"; transcript_biotype "pseudogene";
NZ_CP053601.1	Protein Homology	stop_codon	499100	499102	.	+	0	gene_id "HO397_RS02315"; transcript_id "unassigned_transcript_470"; gbkey "CDS"; gene_biotype "pseudogene"; locus_tag "HO397_RS02315"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_308587.2"; product "RHS repeat-associated core domain-containing protein"; transl_table "11"; exon_number "1"; partial "true"; pseudo "true"; note "incomplete; partial in the middle of a contig; missing N-terminus"; transcript_biotype "pseudogene";
NZ_CP053601.1	RefSeq	gene	2368170	2368245	.	+	.	gene_id "HO397_RS11545"; transcript_id ""; gbkey "Gene"; gene_biotype "tRNA"; locus_tag "HO397_RS11545"; old_locus_tag "HO397_11545";
NZ_CP053601.1	tRNAscan-SE	transcript	2368170	2368245	.	+	.	gene_id "HO397_RS11545"; transcript_id "unassigned_transcript_2337"; gbkey "tRNA"; gene_biotype "tRNA"; locus_tag "HO397_RS11545"; inference "COORDINATES: profile:tRNAscan-SE:2.0.12"; product "tRNA-Val"; transcript_biotype "tRNA"; anticodon "(pos:2368203..2368205)";
NZ_CP053601.1	tRNAscan-SE	exon	2368170	2368245	.	+	.	gene_id "HO397_RS11545"; transcript_id "unassigned_transcript_2337"; gene_biotype "tRNA"; locus_tag "HO397_RS11545"; inference "COORDINATES: profile:tRNAscan-SE:2.0.12"; product "tRNA-Val"; exon_number "1"; transcript_biotype "tRNA"; anticodon "(pos:2368203..2368205)";