Re: [Transdecoder-users] error with cdna_alignment_orf_to_genome_orf.pl
Extracting likely coding regions from transcript sequences
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Re: [Transdecoder-users] error with cdna_alignment_orf_to_genome_orf.pl
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From: Brian H. <bh...@br...> - 2014-02-14 04:22:50
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Hi Will, Can you try using the latest version of the code from sourceforge? Much has changed. If it still doesn't work, we can look into the latest code and try to address it. best, ~brian On Thu, Feb 13, 2014 at 7:54 PM, Will Jackson <wil...@gm...>wrote: > Hi guys, > I am trying to run cdna_alignment_orf_to_genome_orf.pl but am getting > this error: > > Use of uninitialized value $info in pattern match (m//) at > /home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/ > cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1. > Use of uninitialized value $info in concatenation (.) or string at > /home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/ > cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1. > Error, cannot parse ID from at > /home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/ > cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1. > > As inputs I am using are: > GFF3 file produced by transdecoder of transcripts produced by the PASA > annotation comparison and update process. > I used bedtools getfasta -name to get the fasta sequences for the > transcripts produced by PASA. I then ran them through transdecoder to get > the cds and gff3 files, then I used the seqclean utility from trinity to > remove some (195) low quality ORFs. > > The 'transcripts.gff3' file (2nd positional argument) I am using is the > one produced by PASA annotation comparison and update. > > Below is the head of each file: > $ head GG_MAKER_UPDATE_ORFs.transdecoder.gff3 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . gene 315 1454 . - . > ID=g.59;Name=ORF%20g.59%20m.59%20type%3Acomplete%20len%3A380%20%28-%29 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . mRNA 315 1454 . - . ID=m.59;Parent=g.59 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . exon 315 1454 . - . > ID=m.59.exon1;Parent=m.59 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . CDS 315 1454 . - . > ID=cds.m.59;Parent=m.59 > > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . gene 1570 2298 . - . > ID=g.60;Name=ORF%20g.60%20m.60%20type%3Acomplete%20len%3A243%20%28-%29 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . mRNA 1570 2298 . - . ID=m.60;Parent=g.60 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . exon 1570 2298 . - . > ID=m.60.exon1;Parent=m.60 > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18 > . CDS 1570 2298 . - . > ID=cds.m.60;Parent=m.60 > > head APLG003vsItGsH_mydb_pasa.gene_structures_post_PASA_updates.61104.gff3 > ==> APLG003vsItGsH_mydb_pasa.gene_structures_post_PASA_updates.61104.gff3 > <== > # ORIGINAL: genemark-scaffold_1446-processed-gene-0.1-mRNA-1 original gene > structure, not modified by PASA > scaffold_1446 maker gene 6232 6658 . - . > ID=genemark-scaffold_1446-processed-gene-0.1;Name=genemark-scaffold_1446-processed-gene-0.1 > scaffold_1446 maker mRNA 6232 6658 . - . > ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1;Name=genemark-scaffold_1446-processed-gene-0.1 > scaffold_1446 maker exon 6617 6658 . - . > ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1.exon1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 > scaffold_1446 maker CDS 6617 6658 . - 0 > ID=cds.genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 > scaffold_1446 maker exon 6232 6534 . - . > ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1.exon2;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 > scaffold_1446 maker CDS 6232 6534 . - 0 > ID=cds.genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1 > > > #PROT genemark-scaffold_1446-processed-gene-0.1-mRNA-1 > genemark-scaffold_1446-processed-gene-0.1 > MDAEDTRSALIWWKERQGKYPILSSLARDYLACSASSCAAERTFSAAADVCPGNRGKLLPRTIEMCVSSRMWLKDKVPVTGDFEAANNIVQKFTAFKEKNRLNTIDPSPDITKK* > > >m.60 g.60 ORF g.60 m.60 type:complete len:243 (-) > ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18:1570-2298(-) > ATGACCAAACCGTGCGTTCATAATCCCCTCAATTCGTCTCGCCTTGATTCTACGCCTCAG > TTGACAGGATTATACGTGTTGTCACCGAACTTCATCATCTCTAAATATAAGATTACTCAA > TATGACCTTTCGAACGTGTCCACCATACAAAATGCCGCATCAGATTCATTATCCGTCGAT > CCTTCACATCGCCCCATGCCTGGCACAAGATCTCGTGGAGGAGGCGGGGATATGTCATTG > GATCCTCCCATCTCGACTAGCAATGAGAAACCGGTATTGACAAAAAAGTCGAGCATCATT > TTCCCAGTCCCTGTAAATCACTGTAGCATCAGTCCAGACTCAAAATCGATGGTGGCCGTA > GGCGATAGTAGCGAAGTGTTTATATATGACTGTCAAAATGCACATCAATCAAATGAACCG > TTGGTTGGCGATTGGCGATTGGGTCCTCGAAAGATTCATTTACCTGGGGTTTCGCCTCTC > ACCGGTAGCTTTAGTACGAGCTGGAATCAGTATGGAGATAAATTTGCAGTCGCAAGTGAG > > > Am I doing something wrong? > > Thanks > Will > > > > > ------------------------------------------------------------------------------ > Android apps run on BlackBerry 10 > Introducing the new BlackBerry 10.2.1 Runtime for Android apps. > Now with support for Jelly Bean, Bluetooth, Mapview and more. > Get your Android app in front of a whole new audience. Start now. > > http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk > _______________________________________________ > Transdecoder-users mailing list > Tra...@li... > https://lists.sourceforge.net/lists/listinfo/transdecoder-users > > -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
