From: Michał T. L. <m.t...@gm...> - 2019-08-12 02:20:22
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Hi all, I tried to use `generate-names.pl` in the following way: ``` *> /efs/apollo/Nitab-v4.5$ perl ~/tomcat7-deploy/apollo/jbrowse/bin/prepare-refseqs.pl <http://prepare-refseqs.pl> --fasta /efs/apollo/Nitab-v4.5_genome_Chr_Edwards2017.fasta --out /efs/apollo/Nitab-v4.5> /efs/apollo/Nitab-v4.5$ perl ~/tomcat7-deploy/apollo/jbrowse/bin/generate-names.pl <http://generate-names.pl> --tracks Nitab-v4.5_gene_models_Chr_Edwards2017.gff --out /efs/apollo/Nitab-v4.5* ``` on the below GFF3 file: ``` *> cat Nitab-v4.5_gene_models_Chr_Edwards2017.gff...Nt01 maker gene 513567 517023 . - . ID=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080;Parent=Nitab4.5_0002367Nt01 maker mRNA 513567 517023 . - . ID=Nitab4.5_0002367g0080.1;Parent=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080.1;_AED=0.01;_eAED=0.01;_QI=61|1|1|1|1|1|2|173|194;Note="Ribosomal protein S6%2C plastid/chloroplast%2C Translation elongation factor EF1B/ribosomal protein S6%2C Ribosomal protein S6"Nt01 maker exon 513567 513979 . - . ID=Nitab4.5_0002367g0080.1:exon:2876;Parent=Nitab4.5_0002367g0080.1Nt01 maker exon 516618 517023 . - . ID=Nitab4.5_0002367g0080.1:exon:2875;Parent=Nitab4.5_0002367g0080.1Nt01 maker five_prime_UTR 516963 517023 . - . ID=Nitab4.5_0002367g0080.1:five_prime_utr;Parent=Nitab4.5_0002367g0080.1Nt01 maker CDS 516618 516962 . - 0 ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1Nt01 maker CDS 513740 513979 . - 0 ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1Nt01 maker three_prime_UTR 513567 513739 . - . ID=Nitab4.5_0002367g0080.1:three_prime_utr;Parent=Nitab4.5_0002367g0080.1* ``` Unfortunately, it did not work. What did I miss? Thank you in advance. Michal |