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Re: [Gmod-ajax] WARNING: No matching features found for mRNA
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From: Colin <col...@gm...> - 2020-02-02 16:35:16
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This command might appear if your gff3 is not tab separated columns e.g. there are spaces instead of tabs Can you check that the gff is tab separated? -Colin On Sun, Feb 2, 2020 at 11:32 AM Michał T. Lorenc <m.t...@gm...> wrote: > Hi all, > After the running the below command I got *WARNING: No matching features > found for mRNA *and the track is empty: > > > *$ perl ~/tomcat7-deploy/apollo/jbrowse/bin/flatfile-to-json.pl > <http://flatfile-to-json.pl> --nameAttributes "ID,Name,Note" --gff > /efs/apollo/QUT > NbRNASeqAll.sorted-proper.add-rg.bam.dedup.bam.gtf.fasta.transdecoder.genome.FixVSaugustus.hints_utrAGAT.newID-swissprot.filtered.gff3 > --compress --trackType HTMLFeatures --trackLabel > "NbRNASeqAll.sorted-proper.add-rg.bam.dedup.bam.gtf.fasta.transdecoder.genome.FixVSaugustus.hints_utrAGAT.newID-swissprot.filtered" > --type=mRNA --out /efs/apollo/QUTWARNING: No matching features found for > mRNA* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *$ head -n 100 > NbRNASeqAll.sorted-proper.add-rg.bam.dedup.bam.gtf.fasta.transdecoder.genome.FixVSaugustus.hints_utrAGAT.newID-swissprot.filtered.gff3##gff-version > 3##sequence-region NbV1Ch01 1 187320599NbV1Ch01 transdecoder gene 98185 > 99705 . - . ID=NBlab01G00010NbV1Ch01 transdecoder mRNA 98185 99705 . - . > ID=NBlab01G00010.1;Note=Peroxidase 40;Parent=NBlab01G00010NbV1Ch01 > transdecoder exon 98185 98571 . - . > ID=NBlab01G00010.1.exon4;Parent=NBlab01G00010.1NbV1Ch01 transdecoder exon > 98679 98844 . - . ID=NBlab01G00010.1.exon3;Parent=NBlab01G00010.1NbV1Ch01 > transdecoder exon 99134 99325 . - . > ID=NBlab01G00010.1.exon2;Parent=NBlab01G00010.1NbV1Ch01 transdecoder exon > 99417 99705 . - . ID=NBlab01G00010.1.exon1;Parent=NBlab01G00010.1NbV1Ch01 > transdecoder CDS 98186 98571 . - 2 > ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 transdecoder CDS > 98679 98844 . - 0 ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 > transdecoder CDS 99134 99325 . - 0 > ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 transdecoder CDS > 99417 99704 . - 0 ID=NBlab01G00010.1.cds;Parent=NBlab01G00010.1NbV1Ch01 > transdecoder five_prime_UTR 99705 99705 . - . > ID=NBlab01G00010.1.5UTRg1;Parent=NBlab01G00010.1NbV1Ch01 transdecoder > three_prime_UTR 98185 98185 . - . > ID=NBlab01G00010.1.3UTRg1;Parent=NBlab01G00010.1NbV1Ch01 transdecoder gene > 212254 223251 . - . ID=NBlab01G00060NbV1Ch01 transdecoder mRNA 212254 > 223251 . - . ID=NBlab01G00060.1;Note=P34 probable thiol > protease;Parent=NBlab01G00060NbV1Ch01 transdecoder exon 212254 212731 . - . > ID=NBlab01G00060.1.exon5;Parent=NBlab01G00060.1NbV1Ch01 transdecoder exon > 212829 212968 . - . ID=NBlab01G00060.1.exon4;Parent=NBlab01G00060.1NbV1Ch01 > transdecoder exon 218080 219546 . - . > ID=NBlab01G00060.1.exon3;Parent=NBlab01G00060.1NbV1Ch01 transdecoder exon > 219642 222881 . - . ID=NBlab01G00060.1.exon2;Parent=NBlab01G00060.1NbV1Ch01 > transdecoder exon 222989 223251 . - . > ID=NBlab01G00060.1.exon1;Parent=NBlab01G00060.1NbV1Ch01 transdecoder CDS > 219287 219546 . - 2 ID=NBlab01G00060.1.cds;Parent=NBlab01G00060.1NbV1Ch01 > transdecoder CDS 219642 219711 . - 0 > ID=NBlab01G00060.1.cds;Parent=NBlab01G00060.1NbV1Ch01 transdecoder > five_prime_UTR 219712 222881 . - . > ID=NBlab01G00060.1.utr5p2;Parent=NBlab01G00060.1NbV1Ch01 transdecoder > five_prime_UTR 222989 223251 . - . > ID=NBlab01G00060.1.utr5p1;Parent=NBlab01G00060.1NbV1Ch01 transdecoder > three_prime_UTR 212254 212731 . - . > ID=NBlab01G00060.1.utr3p3;Parent=NBlab01G00060.1NbV1Ch01 transdecoder > three_prime_UTR 212829 212968 . - . > ID=NBlab01G00060.1.utr3p2;Parent=NBlab01G00060.1NbV1Ch01 transdecoder > three_prime_UTR 218080 219286 . - . > ID=NBlab01G00060.1.utr3p1;Parent=NBlab01G00060.1NbV1Ch01 transdecoder mRNA > 212254 223251 . - . ID=NBlab01G00060.2;Note=Cysteine proteinase COT44 > %28Fragment%29;Parent=NBlab01G00060NbV1Ch01 transdecoder exon 212254 212731 > . - . ID=NBlab01G00060.2.exon8;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > exon 212829 212968 . - . > ID=NBlab01G00060.2.exon7;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon > 218080 218969 . - . ID=NBlab01G00060.2.exon6;Parent=NBlab01G00060.2NbV1Ch01 > transdecoder exon 219061 219198 . - . > ID=NBlab01G00060.2.exon5;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon > 219271 219546 . - . ID=NBlab01G00060.2.exon4;Parent=NBlab01G00060.2NbV1Ch01 > transdecoder exon 219642 219702 . - . > ID=NBlab01G00060.2.exon3;Parent=NBlab01G00060.2NbV1Ch01 transdecoder exon > 219814 222881 . - . ID=NBlab01G00060.2.exon2;Parent=NBlab01G00060.2NbV1Ch01 > transdecoder exon 222989 223251 . - . > ID=NBlab01G00060.2.exon1;Parent=NBlab01G00060.2NbV1Ch01 transdecoder CDS > 218733 218969 . - 0 ID=NBlab01G00060.2.cds;Parent=NBlab01G00060.2NbV1Ch01 > transdecoder CDS 219061 219198 . - 0 > ID=NBlab01G00060.2.cds;Parent=NBlab01G00060.2NbV1Ch01 transdecoder CDS > 219271 219345 . - 0 ID=NBlab01G00060.2.cds;Parent=NBlab01G00060.2NbV1Ch01 > transdecoder five_prime_UTR 219346 219546 . - . > ID=NBlab01G00060.2.utr5p4;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > five_prime_UTR 219642 219702 . - . > ID=NBlab01G00060.2.utr5p3;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > five_prime_UTR 219814 222881 . - . > ID=NBlab01G00060.2.utr5p2;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > five_prime_UTR 222989 223251 . - . > ID=NBlab01G00060.2.utr5p1;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > three_prime_UTR 212254 212731 . - . > ID=NBlab01G00060.2.utr3p3;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > three_prime_UTR 212829 212968 . - . > ID=NBlab01G00060.2.utr3p2;Parent=NBlab01G00060.2NbV1Ch01 transdecoder > three_prime_UTR 218080 218732 . - . > ID=NBlab01G00060.2.utr3p1;Parent=NBlab01G00060.2NbV1Ch01 transdecoder mRNA > 212254 223251 . - . ID=NBlab01G00060.3;Note=P34 probable thiol > protease;Parent=NBlab01G00060NbV1Ch01 transdecoder exon 212254 212731 . - . > ID=NBlab01G00060.3.exon7;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon > 212829 212968 . - . ID=NBlab01G00060.3.exon6;Parent=NBlab01G00060.3NbV1Ch01 > transdecoder exon 218080 218386 . - . > ID=NBlab01G00060.3.exon5;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon > 219061 219546 . - . ID=NBlab01G00060.3.exon4;Parent=NBlab01G00060.3NbV1Ch01 > transdecoder exon 219642 219702 . - . > ID=NBlab01G00060.3.exon3;Parent=NBlab01G00060.3NbV1Ch01 transdecoder exon > 219866 222881 . - . ID=NBlab01G00060.3.exon2;Parent=NBlab01G00060.3NbV1Ch01 > transdecoder exon 222989 223251 . - . > ID=NBlab01G00060.3.exon1;Parent=NBlab01G00060.3NbV1Ch01 transdecoder CDS > 219287 219546 . - 2 ID=NBlab01G00060.3.cds;Parent=NBlab01G00060.3NbV1Ch01 > transdecoder CDS 219642 219702 . - 0 > ID=NBlab01G00060.3.cds;Parent=NBlab01G00060.3NbV1Ch01 transdecoder CDS > 219866 219940 . - 0 ID=NBlab01G00060.3.cds;Parent=NBlab01G00060.3NbV1Ch01 > transdecoder five_prime_UTR 219941 222881 . - . > ID=NBlab01G00060.3.utr5p2;Parent=NBlab01G00060.3NbV1Ch01 transdecoder > five_prime_UTR 222989 223251 . - . > ID=NBlab01G00060.3.utr5p1;Parent=NBlab01G00060.3NbV1Ch01 transdecoder > three_prime_UTR 212254 212731 . - . > ID=NBlab01G00060.3.utr3p4;Parent=NBlab01G00060.3NbV1Ch01 transdecoder > three_prime_UTR 212829 212968 . - . > ID=NBlab01G00060.3.utr3p3;Parent=NBlab01G00060.3NbV1Ch01 transdecoder > three_prime_UTR 218080 218386 . - . > ID=NBlab01G00060.3.utr3p2;Parent=NBlab01G00060.3NbV1Ch01 transdecoder > three_prime_UTR 219061 219286 . - . > ID=NBlab01G00060.3.utr3p1;Parent=NBlab01G00060.3NbV1Ch01 AUGUSTUS gene > 220636 222022 0.53 + . ID=NBlab01G00070NbV1Ch01 AUGUSTUS mRNA 220636 222022 > 0.1 + . ID=NBlab01G00070.2;Note=P34 probable thiol > protease;Parent=NBlab01G00070NbV1Ch01 AUGUSTUS exon 220636 221012 . + . > ID=NBlab01G00070.2.exon1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS exon > 221193 221357 . + . ID=NBlab01G00070.2.exon2;Parent=NBlab01G00070.2NbV1Ch01 > AUGUSTUS exon 221469 221529 . + . > ID=NBlab01G00070.2.exon3;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS exon > 221625 222022 . + . ID=NBlab01G00070.2.exon4;Parent=NBlab01G00070.2NbV1Ch01 > AUGUSTUS CDS 221010 221012 0.73 + 0 > ID=NBlab01G00070.2.CDS1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS CDS 221193 > 221357 0.72 + 0 ID=NBlab01G00070.2.CDS2;Parent=NBlab01G00070.2NbV1Ch01 > AUGUSTUS CDS 221469 221529 1 + 0 > ID=NBlab01G00070.2.CDS3;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS CDS 221625 > 221884 0.94 + 2 ID=NBlab01G00070.2.CDS4;Parent=NBlab01G00070.2NbV1Ch01 > AUGUSTUS five_prime_utr 220636 221009 0.23 + . > ID=NBlab01G00070.2.5UTR1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS intron > 221013 221192 0.72 + . > ID=NBlab01G00070.2.intron1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS intron > 221358 221468 0.74 + . > ID=NBlab01G00070.2.intron2;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS intron > 221530 221624 1 + . > ID=NBlab01G00070.2.intron3;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS > start_codon 221010 221012 . + 0 > ID=NBlab01G00070.2.SCodon1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS > stop_codon 221882 221884 . + 0 > ID=NBlab01G00070.2.ECodon1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS > three_prime_utr 221885 222022 0.44 + . > ID=NBlab01G00070.2.3UTR1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS > transcription_end_site 222022 222022 . + . > ID=NBlab01G00070.2.TES1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS > transcription_start_site 220636 220636 . + . > ID=NBlab01G00070.2.TSS1;Parent=NBlab01G00070.2NbV1Ch01 AUGUSTUS mRNA 221156 > 222022 0.43 + . ID=NBlab01G00070.1;Note=P34 probable thiol > protease;Parent=NBlab01G00070NbV1Ch01 AUGUSTUS exon 221156 221305 . + . > ID=NBlab01G00070.1.exon1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS exon > 221469 221529 . + . ID=NBlab01G00070.1.exon2;Parent=NBlab01G00070.1NbV1Ch01 > AUGUSTUS exon 221625 222022 . + . > ID=NBlab01G00070.1.exon3;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS CDS 221231 > 221305 1 + 0 ID=NBlab01G00070.1.CDS1;Parent=NBlab01G00070.1NbV1Ch01 > AUGUSTUS CDS 221469 221529 1 + 0 > ID=NBlab01G00070.1.CDS2;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS CDS 221625 > 221884 0.99 + 2 ID=NBlab01G00070.1.CDS3;Parent=NBlab01G00070.1NbV1Ch01 > AUGUSTUS five_prime_utr 221156 221230 0.7 + . > ID=NBlab01G00070.1.5UTR1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS intron > 221306 221468 1 + . > ID=NBlab01G00070.1.intron1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS intron > 221530 221624 1 + . > ID=NBlab01G00070.1.intron2;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS > start_codon 221231 221233 . + 0 > ID=NBlab01G00070.1.SCodon1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS > stop_codon 221882 221884 . + 0 > ID=NBlab01G00070.1.ECodon1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS > three_prime_utr 221885 222022 0.59 + . > ID=NBlab01G00070.1.3UTR1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS > transcription_end_site 222022 222022 . + . > ID=NBlab01G00070.1.TES1;Parent=NBlab01G00070.1NbV1Ch01 AUGUSTUS > transcription_start_site 221156 221156 . + . > ID=NBlab01G00070.1.TSS1;Parent=NBlab01G00070.1...* > > What did I miss? > > Thank you in advance, > > Michal > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
