[Gmod-ajax] WARNING: No matching features found for mRNA

[Michał T. L. <m.t...@gm...>]

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