Empty file generation when i use cdna_alignment_orf_to_genome_orf.pl #203
Description
hi,I'm sorry to bother you.But something has gone wrong.
I do the code software/TransDecoder/util/cdna_alignment_orf_to_genome_orf.pl collapse.collapsed.rep.fa.transdecoder.gff3 transcripts.gff3 collapse.collapsed.rep.fa > transcripts.fasta.transdecoder.genome.gff3
get```
-WARNING, PB.993.9|HiC_scaffold_3:5575287-5577983(-)|transcript/111368 has no genome representation... skipping
-WARNING, PB.994.1|HiC_scaffold_3:6751815-6760957(+)|transcript/11509 has no genome representation... skipping
-WARNING, PB.994.2|HiC_scaffold_3:6754816-6760957(+)|transcript/74478 has no genome representation... skipping
-WARNING, PB.995.1|HiC_scaffold_3:6774170-6788847(+)|transcript/120535 has no genome representation... skipping
-WARNING, PB.996.1|HiC_scaffold_3:6921658-6926049(+)|transcript/19837 has no genome representation... skipping
-WARNING, PB.997.1|HiC_scaffold_3:6940092-6943843(+)|transcript/67803 has no genome representation... skipping
-WARNING, PB.997.1|HiC_scaffold_3:6940092-6943843(+)|transcript/67803 has no genome representation... skipping
-WARNING, PB.997.1|HiC_scaffold_3:6940092-6943843(+)|transcript/67803 has no genome representation... skipping
-WARNING, PB.998.1|HiC_scaffold_3:6957848-6961236(+)|transcript/22563 has no genome representation... skipping
-WARNING, PB.999.1|HiC_scaffold_3:6972946-6976345(+)|transcript/23822 has no genome representation... skipping
Done. 0 / 58379 transcript orfs could be propagated to the genome
`03iso-seq$head transcripts.gff3
==> transcripts.gff3 <==
HiC_scaffold_1 Cufflinks match 44860257 44860601 100 + . ID=GENE^STRG.10986,TRANS^STRG.10986.2;Target=GENE^STRG.10986,TRANS^STRG.10986.2 1 345 +
HiC_scaffold_1 Cufflinks match 44860689 44860825 100 + . ID=GENE^STRG.10986,TRANS^STRG.10986.2;Target=GENE^STRG.10986,TRANS^STRG.10986.2 346 482 +
03iso-seq$ head collapse.collapsed.rep.fa.transdecoder.gff3
PB.1.1|HiC_scaffold_1:16287-22719(+)|transcript/28085 transdecoder gene 1 2982 . - . ID=GENE.PB.1.1|HiC_scaffold_1:16287-22719(+)|transcript/28085
PB.1.1|HiC_scaffold_1:16287-22719(+)|transcript/28085.p1;Name="ORF type:complete (-),score=72.50,evm.model.CTG13557.1|97.3|2.63e-262"
PB.1.1|HiC_scaffold_1:16287-22719(+)|transcript/28085 transdecoder mRNA 1 2982 . - . ID=PB.1.1|HiC_scaffold_1:16287-22719(+)|transcript/28085.p1;Parent=GENE.PB.1.1|HiC_scaffold_1:16287-22719(+)|transcript/28085~~PB.1.1|HiC_scaffold_1:16287-22719(+)|transcript/28085.p1;Name="ORF type:complete (-),score=72.50,evm.model.CTG13557.1|97.3|2.63e-262"
PB.1.1|HiC_scaffold_1:16287-22719(+)|transcript/28085 transdecoder five_prime_UTR 1215 2982 . - . ID=PB.1.1|HiC_scaffold_1:16287-22719(+)|transcript/28085.p1.utr5p1;Parent=PB.1.1|HiC_scaffold_1:16287-22719(+)|transcript/28085.p1
03iso-seq$ head collapse.collapsed.rep.fa
>PB.1.1|HiC_scaffold_1:16287-22719(+)|transcript/28085 transcript/28085 full_length_coverage=2;length=2982
AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTA
AATTTCATCTATTTTAATTATTATTTCAGCAACATGCACACTAGAGAGGATTGGCTTTAC
ATTGTGGTTCCAAGAAGAAATGGTGCGTTAAGATATTCAGACCATTTAAGGTCATCTGGA
TCCCCTTCCAGTGTACGGATTTCAGGTTCTGCATTGGATTTTCCACAATCTATTAGTCCC
CAGGAGTAGACATTGCTTTCAAATTGTAATTCAATACTGCTATTGCTTCCATTGCTGCTG`
and the transcripts.gff3 from stringtie, May I ask if you can provide some assistance? Thank you very much.