ValueError: Can't transform the genomic interval, please check! #69
Description
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)";