i was trying to get transcript file using stringtie then error occured
stringtie output_sorted_bam -o transcripts_gtf -G Piper_nigrum.gff3 -A assembly.txt
WARNING: no reference transcripts were found for the genomic sequences where reads were mapped!
Please make sure the -G annotation file uses the same naming convention for the genome sequences.
i was trying to get transcript file using stringtie then error occured stringtie output_sorted_bam -o transcripts_gtf -G Piper_nigrum.gff3 -A assembly.txt WARNING: no reference transcripts were found for the genomic sequences where reads were mapped! Please make sure the -G annotation file uses the same naming convention for the genome sequences.
these are first few lines of my annotation file
gff-version 3
sequence-region Pn1 10842 48451839
sequence-region Pn10 22 31230699
sequence-region Pn11 16692 29812213
sequence-region Pn12 6065 29594990
sequence-region Pn13 59489 29413843
sequence-region Pn14 9 29032505
sequence-region Pn15 36 28679057
sequence-region Pn16 88635 27941856
sequence-region Pn17 349 25719581
sequence-region Pn18 3990 25553251
sequence-region Pn19 49417 24747179
sequence-region Pn2 6080 43094291
sequence-region Pn20 20749 24277803
sequence-region Pn21 6512 22245691
sequence-region Pn22 10059 22164280
sequence-region Pn23 553 20429441
sequence-region Pn24 19792 19852818
sequence-region Pn25 19625 18169662
sequence-region Pn26 2028 14905565
sequence-region Pn27 24450 29100
sequence-region Pn28 10251 30138
sequence-region Pn29 23182 23388
sequence-region Pn3 2076 39384549
sequence-region Pn30 7548 45795
sequence-region Pn31 2285 44841
sequence-region Pn32 42295 44975
sequence-region Pn33 32 39541
sequence-region Pn34 3251 37613
sequence-region Pn35 30082 30705
sequence-region Pn36 8072 17617
sequence-region Pn37 2184 2625
sequence-region Pn38 28595 29943
sequence-region Pn39 398 28143
sequence-region Pn4 8302 37185481
sequence-region Pn40 16554 17240
sequence-region Pn41 5430 14288
sequence-region Pn42 10727 14243
sequence-region Pn43 22260 22871
sequence-region Pn44 3390 9887
sequence-region Pn45 7058 30162
sequence-region Pn5 157 36774355
sequence-region Pn6 6382 33605596
sequence-region Pn7 2534 32736002
sequence-region Pn8 44 32719039
sequence-region Pn9 128 32482198
Pn1 EVM mRNA 10842 11267 . + . ID=evm.model.Pn1.1 Pn1 EVM exon 10842 11267 . + . ID=evm.model.Pn1.1.exon1;Parent=evm.model.Pn1.1 Pn1 EVM CDS 10842 11267 . + 0 ID=cds.evm.model.Pn1.1;Parent=evm.model.Pn1.1
Pn1 EVM mRNA 19952 20188 . + . ID=evm.model.Pn1.2 Pn1 EVM exon 19952 20188 . + . ID=evm.model.Pn1.2.exon1;Parent=evm.model.Pn1.2 Pn1 EVM CDS 19952 20188 . + 0 ID=cds.evm.model.Pn1.2;Parent=evm.model.Pn1.2
Pn1 EVM mRNA 67496 68035 . - . ID=evm.model.Pn1.3 Pn1 EVM exon 67496 68035 . - . ID=evm.model.Pn1.3.exon1;Parent=evm.model.Pn1.3 Pn1 EVM CDS 67496 68035 . - 0 ID=cds.evm.model.Pn1.3;Parent=evm.model.Pn1.3
Pn1 EVM mRNA 68921 69345 . - . ID=evm.model.Pn1.4 Pn1 EVM exon 68921 69087 . - . ID=evm.model.Pn1.4.exon2;Parent=evm.model.Pn1.4 Pn1 EVM CDS 68921 69087 . - 2 ID=cds.evm.model.Pn1.4;Parent=evm.model.Pn1.4 Pn1 EVM exon 69249 69345 . - . ID=evm.model.Pn1.4.exon1;Parent=evm.model.Pn1.4 Pn1 EVM CDS 69249 69345 . - 0 ID=cds.evm.model.Pn1.4;Parent=evm.model.Pn1.4
Pn1 EVM mRNA 73564 74589 . - . ID=evm.model.Pn1.5 Pn1 EVM exon 73564 74589 . - . ID=evm.model.Pn1.5.exon1;Parent=evm.model.Pn1.5 Pn1 EVM CDS 73564 74589 . - 0 ID=cds.evm.model.Pn1.5;Parent=evm.model.Pn1.5
Pn1 EVM mRNA 76279 78348 . - . ID=evm.model.Pn1.6 Pn1 EVM exon 76279 77882 . - . ID=evm.model.Pn1.6.exon3;Parent=evm.model.Pn1.6 Pn1 EVM CDS 76279 77882 . - 2 ID=cds.evm.model.Pn1.6;Parent=evm.model.Pn1.6 Pn1 EVM exon 77981 78152 . - . ID=evm.model.Pn1.6.exon2;Parent=evm.model.Pn1.6 Pn1 EVM CDS 77981 78152 . - 0 ID=cds.evm.model.Pn1.6;Parent=evm.model.Pn1.6 Pn1 EVM exon 78241 78348 . - . ID=evm.model.Pn1.6.exon1;Parent=evm.model.Pn1.6 Pn1 EVM CDS 78241 78348 . - 0 ID=cds.evm.model.Pn1.6;Parent=evm.model.Pn1.6
Pn1 EVM mRNA 78599 80899 . + . ID=evm.model.Pn1.7 Pn1 EVM exon 78599 80899 . + . ID=evm.model.Pn1.7.exon1;Parent=evm.model.Pn1.7 Pn1 EVM CDS 78599 80899 . + 0 ID=cds.evm.model.Pn1.7;Parent=evm.model.Pn1.7
Pn1 EVM mRNA 94000 97630 . - . ID=evm.model.Pn1.8 Pn1 EVM exon 94000 94039 . - . ID=evm.model.Pn1.8.exon6;Parent=evm.model.Pn1.8 Pn1 EVM CDS 94000 94039 . - 1 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8 Pn1 EVM exon 94111 94173 . - . ID=evm.model.Pn1.8.exon5;Parent=evm.model.Pn1.8 Pn1 EVM CDS 94111 94173 . - 1 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8 Pn1 EVM exon 95257 95328 . - . ID=evm.model.Pn1.8.exon4;Parent=evm.model.Pn1.8 Pn1 EVM CDS 95257 95328 . - 1 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8 Pn1 EVM exon 95706 95782 . - . ID=evm.model.Pn1.8.exon3;Parent=evm.model.Pn1.8 Pn1 EVM CDS 95706 95782 . - 0 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8 Pn1 EVM exon 97358 97453 . - . ID=evm.model.Pn1.8.exon2;Parent=evm.model.Pn1.8 Pn1 EVM CDS 97358 97453 . - 0 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8 Pn1 EVM exon 97568 97630 . - . ID=evm.model.Pn1.8.exon1;Parent=evm.model.Pn1.8 Pn1 EVM CDS 97568 97630 . - 0 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8
Pn1 EVM mRNA 99324 103009 . - . ID=evm.model.Pn1.9 Pn1 EVM exon 99324 99436 . - . ID=evm.model.Pn1.9.exon3;Parent=evm.model.Pn1.9 Pn1 EVM CDS 99324 99436 . - 1 ID=cds.evm.model.Pn1.9;Parent=evm.model.Pn1.9 Pn1 EVM exon 100641 100687 . - . ID=evm.model.Pn1.9.exon2;Parent=evm.model.Pn1.9 Pn1 EVM CDS 100641 100687 . - 0 ID=cds.evm.model.Pn1.9;Parent=evm.model.Pn1.9 Pn1 EVM exon 102917 103009 . - . ID=evm.model.Pn1.9.exon1;Parent=evm.model.Pn1.9 Pn1 EVM CDS 102917 103009 . - 0 ID=cds.evm.model.Pn1.9;Parent=evm.model.Pn1.9
Pn1 EVM mRNA 115756 116324 . - . ID=evm.model.Pn1.10 Pn1 EVM exon 115756 115776 . - . ID=evm.model.Pn1.10.exon2;Parent=evm.model.Pn1.10 Pn1 EVM CDS 115756 115776 . - 0 ID=cds.evm.model.Pn1.10;Parent=evm.model.Pn1.10 Pn1 EVM exon 116115 116324 . - . ID=evm.model.Pn1.10.exon1;Parent=evm.model.Pn1.10 Pn1 EVM CDS 116115 116324 . - 0 ID=cds.evm.model.Pn1.10;Parent=evm.model.Pn1.10