; parse-gtf -v 2 -i $RSAT/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60.gtf -fasta $RSAT/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60.pep.all.fa -org_name Populus_trichocarpa.Pop_tri_v4.60 -task all -taxid 3694 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome ; Program version 1.48 ; Input files ; fasta_rm /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60.dna_rm.genome.fa ; fasta_pep /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60.pep.all.fa ; fasta /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60.dna.toplevel.fa ; gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60.gtf ; Output files ; gene_gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60_gene.gtf ; log /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/log.txt ; gene_end_gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60_gene_end.gtf ; fasta_lengths /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60.dna.toplevel_lengths.tab ; cds /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/cds.tab ; fasta_rm_lengths /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60.dna_rm.genome_lengths.tab ; contig_rm /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/contig_rm.tab ; five_prime_utr_gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60_five_prime_utr.gtf ; transcript_gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60_transcript.gtf ; stop_codon_gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60_stop_codon.gtf ; start_codon /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/start_codon.tab ; tss_gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60_tss.gtf ; contigs_txt /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/contigs.txt ; exon_gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60_exon.gtf ; three_prime_utr_gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60_three_prime_utr.gtf ; start_codon_gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60_start_codon.gtf ; contig /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/contig.tab ; organism /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/organism.tab ; exon /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/exon.tab ; gene_start_gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60_gene_start.gtf ; contigs_txt_rm /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/contigs_rm.txt ; stop_codon /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/stop_codon.tab ; transcript /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/transcript.tab ; gene /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/gene.tab ; tts_gtf /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60_tts.gtf ; fasta_pep_lengths /var/www/html/rsat/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/Populus_trichocarpa.Pop_tri_v4.60.pep.all_lengths.tab ; peptidic_sequences /var/www/html/rsat/public_html/data/genomes/Populus_trichocarpa.Pop_tri_v4.60/genome/peptidic_sequences.fasta ; Parsed rows per feature type ; cds 309929 ; exon 333784 ; five_prime_utr 62804 ; gene 34699 ; start_codon 52404 ; stop_codon 52429 ; three_prime_utr 56224 ; transcript 52400 ; Parsed rows per contig ; Contig Total cds exon five_prime_utr gene start stop three_prime_utr transcript ; 1 116617 38313 41299 7559 4074 6215 6234 6704 6219 ; 10 66861 21964 23719 4375 2299 3548 3542 3870 3544 ; 11 39802 12825 13870 2634 1470 2207 2208 2380 2208 ; 12 33433 10705 11533 2195 1248 1905 1918 2024 1905 ; 13 36959 11888 12803 2434 1393 2082 2084 2195 2080 ; 14 46979 15332 16482 3077 1673 2556 2561 2745 2553 ; 15 37515 12562 13452 2343 1264 1934 1938 2088 1934 ; 16 31466 9963 10741 2151 1243 1811 1812 1934 1811 ; 17 29961 9238 9949 2070 1290 1830 1822 1934 1828 ; 18 36563 11972 12916 2431 1293 1946 1945 2112 1948 ; 19 28947 8829 9710 2105 1177 1746 1746 1887 1747 ; 2 65659 21510 23081 4214 2347 3548 3544 3872 3543 ; 3 56974 18681 20139 3724 1968 3051 3058 3298 3055 ; 4 53783 17412 18642 3476 2078 3014 3017 3129 3015 ; 5 61653 19887 21411 4170 2247 3422 3422 3671 3423 ; 6 70977 23119 24912 4716 2524 3853 3847 4158 3848 ; 7 36497 11847 12692 2330 1367 2034 2037 2154 2036 ; 8 58882 19505 20850 3719 2039 3154 3151 3309 3155 ; 9 40131 12950 13923 2686 1494 2234 2231 2380 2233 ; scaffold_104 471 127 143 41 25 35 34 31 35 ; scaffold_1549 14 2 2 1 2 2 2 1 2 ; scaffold_1697 7 1 1 1 1 1 1 0 1 ; scaffold_1865 226 71 79 18 9 13 13 10 13 ; scaffold_1944 6 1 1 0 1 1 1 0 1 ; scaffold_2281 53 13 16 4 1 4 4 7 4 ; scaffold_25 1367 340 451 129 59 85 85 133 85 ; scaffold_3435 37 9 9 2 3 4 4 2 4 ; scaffold_45 491 125 154 41 17 35 35 49 35 ; scaffold_502 360 107 115 22 18 24 24 26 24 ; scaffold_509 457 161 170 25 17 21 21 20 22 ; scaffold_522 40 9 9 3 4 5 4 1 5 ; scaffold_67 939 285 324 74 30 53 53 67 53 ; scaffold_780 330 112 119 20 12 16 16 19 16 ; scaffold_820 216 64 67 14 12 15 15 14 15 ; Host name baobab ; Job started 2024-11-29.110823 ; Job done 2024-11-29.114154 ; Seconds 66.49 ; user 66.49 ; system 2.56 ; cuser 3027.35 ; csystem 157.99