; parse-gtf -v 2 -i $RSAT/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40.gtf -fasta $RSAT/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40.pep.all.fa -org_name Oryza_brachyantha.Oryza_brachyantha.v1.4b.40 -task all -taxid 4533 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome ; Program version 1.48 ; Input files ; fasta_rm /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40.dna_rm.genome.fa ; gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40.gtf ; fasta /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40.dna.toplevel.fa ; fasta_pep /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40.pep.all.fa ; Output files ; peptidic_sequences /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/peptidic_sequences.fasta ; contigs_txt_rm /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/contigs_rm.txt ; tts_gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40_tts.gtf ; gene_gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40_gene.gtf ; contig_rm /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/contig_rm.tab ; gene /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/gene.tab ; stop_codon_gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40_stop_codon.gtf ; transcript /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/transcript.tab ; gene_start_gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40_gene_start.gtf ; gene_end_gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40_gene_end.gtf ; cds /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/cds.tab ; three_prime_utr_gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40_three_prime_utr.gtf ; log /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/log.txt ; exon /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/exon.tab ; organism /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/organism.tab ; contig /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/contig.tab ; tss_gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40_tss.gtf ; stop_codon /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/stop_codon.tab ; start_codon_gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40_start_codon.gtf ; five_prime_utr_gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40_five_prime_utr.gtf ; transcript_gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40_transcript.gtf ; fasta_lengths /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40.dna.toplevel_lengths.tab ; start_codon /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/start_codon.tab ; contigs_txt /var/www/html/rsat/public_html/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/contigs.txt ; fasta_pep_lengths /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40.pep.all_lengths.tab ; fasta_rm_lengths /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40.dna_rm.genome_lengths.tab ; exon_gtf /var/www/html/rsat/data/genomes/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40/genome/Oryza_brachyantha.Oryza_brachyantha.v1.4b.40_exon.gtf ; Parsed rows per feature type ; cds 146785 ; exon 169571 ; five_prime_utr 7789 ; gene 34598 ; start_codon 30492 ; stop_codon 30370 ; three_prime_utr 12391 ; transcript 34598 ; Parsed rows per contig ; Contig Total cds exon five_prime_utr gene start stop three_prime_utr transcript ; 1 66377 21018 24243 1114 4818 4283 4278 1805 4818 ; 10 23543 7355 8373 322 1863 1625 1598 544 1863 ; 11 24285 7463 8509 331 1984 1737 1718 559 1984 ; 12 24679 7797 8930 384 1841 1624 1642 620 1841 ; 2 53958 17064 19874 989 3868 3393 3398 1504 3868 ; 3 60060 19028 22280 1193 4189 3712 3709 1760 4189 ; 4 40776 12755 14793 664 3055 2675 2661 1118 3055 ; 5 37744 11875 13749 662 2779 2461 2427 1012 2779 ; 6 37650 11879 13624 595 2814 2495 2482 947 2814 ; 7 33771 10757 12325 521 2459 2187 2182 881 2459 ; 8 30166 9379 10892 514 2269 2007 2009 827 2269 ; 9 24951 7847 9036 405 1861 1655 1636 650 1861 ; JH369865.2 225 81 87 2 13 12 13 4 13 ; JH369866.2 74 23 27 1 5 5 5 3 5 ; JH369869.2 116 40 45 2 8 5 6 2 8 ; JH369872.2 283 87 107 7 18 17 17 12 18 ; JH369873.2 165 51 59 5 12 11 12 3 12 ; JH369874.2 90 25 29 2 8 8 8 2 8 ; JH369876.2 99 33 36 1 7 6 7 2 7 ; JH369879.2 29 9 9 0 3 3 2 0 3 ; JH369881.2 165 58 65 1 9 8 9 6 9 ; JH369887.2 85 29 29 0 7 6 7 0 7 ; JH369888.2 28 10 12 1 1 1 1 1 1 ; JH369889.2 136 36 38 0 15 15 15 2 15 ; JH369897.2 38 13 13 0 3 3 3 0 3 ; JH369902.2 101 34 39 1 6 6 5 4 6 ; JH369904.2 30 12 13 0 1 1 1 1 1 ; JH369905.2 76 19 25 2 7 6 6 4 7 ; JH369906.2 44 13 16 1 3 3 3 2 3 ; JH369909.2 34 8 11 1 3 3 3 2 3 ; JH369912.2 44 13 14 1 4 4 4 0 4 ; JH369919.2 54 18 20 1 4 4 2 1 4 ; JH369920.2 57 10 19 1 10 3 3 1 10 ; JH369922.2 161 52 57 1 12 11 12 4 12 ; JH369927.2 114 36 43 1 8 6 7 5 8 ; JH369928.2 75 28 28 0 5 5 4 0 5 ; JH369930.2 42 12 13 0 4 4 4 1 4 ; JH369936.2 74 24 25 0 6 6 6 1 6 ; JH369937.2 26 7 9 0 2 2 2 2 2 ; JH369939.2 49 15 17 1 4 4 3 1 4 ; JH369941.2 20 7 8 0 1 1 1 1 1 ; JH369944.2 22 5 7 1 2 2 2 1 2 ; JH369947.2 34 11 11 0 3 3 3 0 3 ; JH369948.2 18 7 7 0 1 1 1 0 1 ; JH369949.2 40 10 15 3 3 2 2 2 3 ; JH369950.2 11 2 2 0 2 2 1 0 2 ; JH369951.2 14 3 3 0 2 2 2 0 2 ; JH369953.2 100 29 37 4 8 6 5 3 8 ; JH369954.2 8 2 2 0 1 1 1 0 1 ; JH369956.2 23 4 4 0 4 3 4 0 4 ; JH369966.2 76 19 22 1 8 8 8 2 8 ; JH369967.2 6 1 1 0 1 1 1 0 1 ; JH369969.2 22 8 8 0 2 1 1 0 2 ; JH369970.2 93 29 33 1 7 6 7 3 7 ; JH369971.2 26 9 11 1 1 1 1 1 1 ; JH369972.2 53 13 13 0 7 6 7 0 7 ; JH369974.2 24 10 10 0 1 1 1 0 1 ; JH369980.2 9 3 3 0 1 0 1 0 1 ; JH369984.2 88 33 38 1 3 3 3 4 3 ; JH369985.2 37 13 13 0 3 3 2 0 3 ; JH369987.2 32 12 12 0 2 2 2 0 2 ; JH369989.2 69 20 23 2 6 6 5 1 6 ; JH369992.2 54 15 17 0 5 5 5 2 5 ; JH369994.2 29 7 7 0 4 3 4 0 4 ; JH369997.2 75 28 30 1 4 4 3 1 4 ; JH370001.2 14 3 3 0 2 2 2 0 2 ; JH370004.2 36 10 13 2 3 2 2 1 3 ; JH370005.2 35 8 10 1 4 4 3 1 4 ; JH370013.2 8 2 2 0 1 1 1 0 1 ; JH370025.2 61 18 21 1 5 5 4 2 5 ; JH370026.2 22 4 4 0 4 3 3 0 4 ; JH370029.2 162 50 57 3 12 12 12 4 12 ; JH370034.2 10 3 3 0 1 1 1 0 1 ; JH370038.2 20 5 6 1 2 2 2 0 2 ; JH370040.2 16 6 6 0 1 1 1 0 1 ; JH370041.2 6 1 1 0 1 1 1 0 1 ; JH370046.2 15 2 3 0 3 2 2 0 3 ; JH370047.2 8 2 2 0 1 1 1 0 1 ; JH370048.2 21 9 9 0 1 1 0 0 1 ; JH370051.2 17 4 5 1 2 2 1 0 2 ; JH370052.2 32 12 12 0 2 2 2 0 2 ; JH370053.2 12 3 3 0 2 1 1 0 2 ; JH370054.2 9 0 3 0 3 0 0 0 3 ; JH370056.2 25 6 7 0 3 2 3 1 3 ; JH370061.2 32 14 14 0 1 1 1 0 1 ; JH370062.2 12 4 4 0 1 1 1 0 1 ; JH370067.2 11 4 4 0 1 1 0 0 1 ; JH370071.2 3 0 1 0 1 0 0 0 1 ; JH370074.2 6 1 1 0 1 1 1 0 1 ; JH370079.2 6 1 1 0 1 1 1 0 1 ; JH370084.2 8 2 2 0 1 1 1 0 1 ; JH370087.2 26 9 9 0 2 2 2 0 2 ; JH370088.2 16 3 5 1 2 1 1 1 2 ; JH370089.2 6 1 1 0 1 1 1 0 1 ; JH370107.2 3 0 1 0 1 0 0 0 1 ; JH370118.2 3 0 1 0 1 0 0 0 1 ; JH592213.1 51 10 14 1 6 6 6 2 6 ; JH592215.1 44 14 16 1 3 3 3 1 3 ; JH592216.1 14 5 5 0 1 1 1 0 1 ; JH592217.1 37 10 12 0 4 3 3 1 4 ; JH592218.1 38 11 13 0 3 3 3 2 3 ; JH592219.1 30 9 9 0 3 3 3 0 3 ; JH592220.1 26 11 11 0 1 1 1 0 1 ; JH592221.1 18 5 5 0 2 2 2 0 2 ; JH592223.1 16 4 4 0 2 2 2 0 2 ; JH592224.1 12 4 4 0 1 1 1 0 1 ; JH592225.1 18 5 5 0 2 2 2 0 2 ; JH592227.1 30 6 6 0 5 4 4 0 5 ; JH592228.1 14 3 3 0 2 2 2 0 2 ; JH592231.1 8 2 2 0 1 1 1 0 1 ; JH592234.1 39 9 12 2 4 4 3 1 4 ; JH592235.1 38 17 17 0 1 1 1 0 1 ; JH592236.1 9 3 3 0 1 1 0 0 1 ; JH592238.1 9 3 3 0 1 1 0 0 1 ; JH592239.1 20 4 4 0 3 3 3 0 3 ; JH592241.1 6 1 1 0 1 1 1 0 1 ; JH592244.1 8 2 2 0 1 1 1 0 1 ; JH592245.1 12 5 5 0 1 0 0 0 1 ; JH592246.1 20 8 8 0 1 1 1 0 1 ; JH592247.1 12 2 2 0 2 2 2 0 2 ; JH592252.1 8 2 2 0 1 1 1 0 1 ; JH592254.1 10 3 3 0 1 1 1 0 1 ; JH592255.1 14 5 5 0 1 1 1 0 1 ; JH592258.1 24 10 10 0 1 1 1 0 1 ; JH592259.1 10 3 3 0 1 1 1 0 1 ; JH592262.1 6 1 1 0 1 1 1 0 1 ; JH592263.1 24 9 10 1 1 1 1 0 1 ; JH592265.1 6 1 1 0 1 1 1 0 1 ; JH592267.1 16 6 6 0 1 1 1 0 1 ; JH592268.1 6 1 1 0 1 1 1 0 1 ; JH592269.1 10 3 3 0 1 1 1 0 1 ; JH592271.1 6 1 1 0 1 1 1 0 1 ; JH592272.1 22 9 9 0 1 1 1 0 1 ; JH592273.1 6 1 1 0 1 1 1 0 1 ; JH592274.1 5 1 1 0 1 0 1 0 1 ; JH592275.1 4 1 1 0 1 0 0 0 1 ; JH592276.1 6 1 1 0 1 1 1 0 1 ; JH592277.1 11 2 2 0 2 2 1 0 2 ; JH592280.1 12 4 4 0 1 1 1 0 1 ; JH592281.1 4 1 1 0 1 0 0 0 1 ; JH592282.1 14 3 5 1 1 1 1 1 1 ; JH592284.1 6 1 1 0 1 1 1 0 1 ; JH592285.1 20 7 8 0 1 1 1 1 1 ; JH592286.1 6 1 1 0 1 1 1 0 1 ; JH592287.1 13 3 3 0 2 1 2 0 2 ; JH592289.1 5 1 1 0 1 1 0 0 1 ; JH592291.1 8 2 2 0 1 1 1 0 1 ; JH592294.1 6 1 1 0 1 1 1 0 1 ; JH592296.1 8 2 2 0 1 1 1 0 1 ; JH592297.1 6 1 1 0 1 1 1 0 1 ; JH592299.1 8 2 2 0 1 1 1 0 1 ; JH592302.1 8 3 3 0 1 0 0 0 1 ; JH592550.1 3 0 1 0 1 0 0 0 1 ; JH593152.1 3 0 1 0 1 0 0 0 1 ; JH593233.1 3 0 1 0 1 0 0 0 1 ; super0037 577 173 189 5 55 47 47 6 55 ; super0038 136 36 47 3 15 9 9 2 15 ; super0042 106 31 33 0 10 10 10 2 10 ; super0043 183 66 72 3 10 9 10 3 10 ; super0044 305 82 94 5 30 30 27 7 30 ; super0045 45 11 13 0 7 3 4 0 7 ; super0050 62 20 21 0 5 5 5 1 5 ; super0051 81 20 23 0 9 9 8 3 9 ; super0053 118 32 43 4 9 7 7 7 9 ; super0056 56 17 19 0 6 4 4 0 6 ; super0057 56 20 21 0 4 3 3 1 4 ; super0058 80 32 34 0 3 3 3 2 3 ; super0060 20 7 7 0 2 1 1 0 2 ; super0062 23 8 9 0 2 1 1 0 2 ; super0063 18 7 7 0 1 1 1 0 1 ; super0068 38 10 11 0 4 4 4 1 4 ; super0069 32 8 8 1 4 3 4 0 4 ; super0070 30 13 13 0 1 1 1 0 1 ; super0072 62 20 21 0 5 5 5 1 5 ; super0073 82 31 35 2 3 3 3 2 3 ; super0074 53 15 18 0 6 4 3 1 6 ; super0075 46 13 18 2 4 2 2 1 4 ; super0077 79 22 28 1 8 5 5 2 8 ; super0078 50 15 17 1 4 4 4 1 4 ; super0079 46 15 15 0 4 4 4 0 4 ; super0080 24 7 8 0 2 2 2 1 2 ; super0085 23 8 8 0 2 2 1 0 2 ; super0089 6 1 1 0 1 1 1 0 1 ; super0090 28 8 8 0 3 3 3 0 3 ; super0092 61 21 21 0 5 5 4 0 5 ; super0093 108 38 40 0 8 6 7 1 8 ; super0094 8 2 2 0 1 1 1 0 1 ; super0095 22 5 5 0 3 3 3 0 3 ; super0100 10 2 2 0 2 0 2 0 2 ; super0104 40 12 12 0 4 4 4 0 4 ; super0107 20 6 8 1 1 1 1 1 1 ; super0116 110 39 45 1 6 5 4 4 6 ; super0117 54 21 21 0 3 3 3 0 3 ; super0119 57 15 16 0 7 6 6 0 7 ; super0126 12 2 2 0 2 2 2 0 2 ; super0129 6 1 1 0 1 1 1 0 1 ; super0134 18 5 5 0 2 2 2 0 2 ; super0137 44 12 14 1 4 4 4 1 4 ; super0139 12 2 2 0 2 2 2 0 2 ; super0140 22 7 7 0 2 2 2 0 2 ; super0143 8 2 2 0 1 1 1 0 1 ; super0152 10 3 3 0 1 1 1 0 1 ; super0153 16 4 4 0 2 2 2 0 2 ; super0160 10 3 3 0 1 1 1 0 1 ; super0161 18 4 6 0 3 1 1 0 3 ; super0168 66 22 23 0 5 5 5 1 5 ; super0171 42 15 15 0 3 3 3 0 3 ; super0176 66 11 23 1 11 3 3 3 11 ; super0177 16 6 6 0 1 1 1 0 1 ; super0178 8 2 2 0 1 1 1 0 1 ; super0189 18 6 7 0 1 1 1 1 1 ; super0191 26 8 9 0 2 2 2 1 2 ; super0194 34 8 9 0 4 4 4 1 4 ; super0199 27 1 8 0 8 1 1 0 8 ; super0207 26 4 6 0 5 3 3 0 5 ; super0224 6 1 1 0 1 1 1 0 1 ; super0240 12 0 4 0 4 0 0 0 4 ; super0245 7 2 2 0 1 1 0 0 1 ; super0433 9 0 3 0 3 0 0 0 3 ; super0520 6 0 2 0 2 0 0 0 2 ; super0638 12 0 4 0 4 0 0 0 4 ; super1266 3 0 1 0 1 0 0 0 1 ; super1358 3 0 1 0 1 0 0 0 1 ; super1388 3 0 1 0 1 0 0 0 1 ; super1581 3 0 1 0 1 0 0 0 1 ; super1614 3 0 1 0 1 0 0 0 1 ; super1643 3 0 1 0 1 0 0 0 1 ; super1674 6 0 2 0 2 0 0 0 2 ; super1867 3 0 1 0 1 0 0 0 1 ; super2144 6 0 2 0 2 0 0 0 2 ; super2603 3 0 1 0 1 0 0 0 1 ; super2680 3 0 1 0 1 0 0 0 1 ; super3219 3 0 1 0 1 0 0 0 1 ; super3319 3 0 1 0 1 0 0 0 1 ; super3764 3 0 1 0 1 0 0 0 1 ; super3790 3 0 1 0 1 0 0 0 1 ; super3972 3 0 1 0 1 0 0 0 1 ; super4171 3 0 1 0 1 0 0 0 1 ; super4184 3 0 1 0 1 0 0 0 1 ; super4362 3 0 1 0 1 0 0 0 1 ; super4399 3 0 1 0 1 0 0 0 1 ; super4668 3 0 1 0 1 0 0 0 1 ; super4691 3 0 1 0 1 0 0 0 1 ; super5368 6 0 2 0 2 0 0 0 2 ; super5463 3 0 1 0 1 0 0 0 1 ; super5714 6 0 2 0 2 0 0 0 2 ; super5788 3 0 1 0 1 0 0 0 1 ; super5871 3 0 1 0 1 0 0 0 1 ; super6095 3 0 1 0 1 0 0 0 1 ; super6801 9 0 3 0 3 0 0 0 3 ; super7393 3 0 1 0 1 0 0 0 1 ; Host name baobab.eead.csic.es ; Job started 2018-09-21.093828 ; Job done 2018-09-21.131122 ; Seconds 58.14 ; user 58.14 ; system 3.73 ; cuser 12624.2 ; csystem 137.88