; parse-gtf -v 2 -i $RSAT/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60.gtf -fasta $RSAT/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60.pep.all.fa -org_name Gossypium_raimondii.Graimondii2_0_v6.60 -task all -taxid 29730 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome ; Program version 1.48 ; Input files ; gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60.gtf ; fasta_pep /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60.pep.all.fa ; fasta /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60.dna.toplevel.fa ; fasta_rm /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60.dna_rm.genome.fa ; Output files ; contig_rm /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/contig_rm.tab ; cds /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/cds.tab ; peptidic_sequences /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/peptidic_sequences.fasta ; transcript_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60_transcript.gtf ; gene /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/gene.tab ; three_prime_utr_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60_three_prime_utr.gtf ; gene_start_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60_gene_start.gtf ; gene_end_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60_gene_end.gtf ; five_prime_utr_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60_five_prime_utr.gtf ; exon_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60_exon.gtf ; tts_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60_tts.gtf ; contig /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/contig.tab ; organism /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/organism.tab ; log /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/log.txt ; fasta_lengths /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60.dna.toplevel_lengths.tab ; fasta_rm_lengths /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60.dna_rm.genome_lengths.tab ; fasta_pep_lengths /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60.pep.all_lengths.tab ; start_codon_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60_start_codon.gtf ; stop_codon /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/stop_codon.tab ; contigs_txt /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/contigs.txt ; gene_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60_gene.gtf ; contigs_txt_rm /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/contigs_rm.txt ; transcript /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/transcript.tab ; exon /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/exon.tab ; tss_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60_tss.gtf ; stop_codon_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/Gossypium_raimondii.Graimondii2_0_v6.60_stop_codon.gtf ; start_codon /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0_v6.60/genome/start_codon.tab ; Parsed rows per feature type ; cds 485692 ; exon 485865 ; five_prime_utr 58224 ; gene 38208 ; start_codon 75889 ; stop_codon 36553 ; three_prime_utr 60522 ; transcript 78371 ; Parsed rows per contig ; Contig Total cds exon five_prime_utr gene start stop three_prime_utr transcript ; 1 94216 34388 34400 4291 2804 5533 2619 4487 5694 ; 10 92645 34357 34367 3966 2642 5221 2541 4098 5453 ; 11 98600 36459 36467 4168 3028 5576 2705 4372 5825 ; 12 63050 22892 22901 2895 1918 3763 1823 2980 3878 ; 13 93337 34115 34124 4235 2773 5463 2628 4365 5634 ; 2 94234 34989 35003 4037 2745 5249 2580 4200 5431 ; 3 67294 24697 24705 3011 1909 3895 1929 3106 4042 ; 4 105244 38965 38985 4589 2993 5931 2821 4813 6147 ; 5 90066 32655 32676 4124 2745 5389 2654 4277 5546 ; 6 102069 37936 37947 4426 2794 5739 2719 4616 5892 ; 7 131894 48596 48609 5750 3865 7577 3633 6052 7812 ; 8 111427 40977 40991 5021 3030 6498 3081 5194 6635 ; 9 169801 62886 62909 7454 4639 9665 4621 7708 9919 ; KB204119 1725 610 610 80 60 111 51 87 116 ; KB204120 765 273 273 31 26 51 24 34 53 ; KB204121 185 69 69 8 5 11 4 7 12 ; KB204123 27 7 7 1 3 3 2 1 3 ; KB204124 62 25 25 0 3 3 1 2 3 ; KB204125 34 9 9 2 4 3 1 2 4 ; KB204127 86 27 27 3 6 6 5 5 7 ; KB204128 18 4 4 2 2 2 0 2 2 ; KB204129 24 6 6 2 2 2 1 2 3 ; KB204131 12 2 2 2 2 1 1 0 2 ; 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KB204848 12 4 4 1 1 1 0 0 1 ; KB204877 10 2 2 1 1 1 1 1 1 ; KB204890 13 4 4 0 2 0 1 0 2 ; KB204910 12 3 3 1 1 1 1 1 1 ; KB204922 8 1 1 1 1 1 1 1 1 ; KB204924 15 2 2 2 2 2 1 2 2 ; KB204933 11 2 2 1 2 1 1 0 2 ; KB204938 7 2 2 0 1 1 0 0 1 ; KB204971 6 1 1 0 1 1 1 0 1 ; Host name baobab ; Job started 2024-11-29.131357 ; Job done 2024-11-29.135332 ; Seconds 106.05 ; user 106.05 ; system 8.19 ; cuser 3435.95 ; csystem 191.8