; parse-gtf -v 2 -i $RSAT/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109.gtf -fasta $RSAT/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109.pep.all.fa -org_name Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109 -task all -taxid 9031 -gtf_source Ensembl -o $RSAT/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome ; Program version 1.48 ; Input files ; fasta_rm /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109.dna_rm.genome.fa ; gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109.gtf ; fasta /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109.dna.toplevel.fa ; fasta_pep /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109.pep.all.fa ; Output files ; fasta_lengths /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109.dna.toplevel_lengths.tab ; gene /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/gene.tab ; contig /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/contig.tab ; tss_gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109_tss.gtf ; gene_start_gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109_gene_start.gtf ; tts_gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109_tts.gtf ; exon_gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109_exon.gtf ; start_codon /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/start_codon.tab ; transcript /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/transcript.tab ; start_codon_gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109_start_codon.gtf ; stop_codon /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/stop_codon.tab ; organism /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/organism.tab ; peptidic_sequences /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/peptidic_sequences.fasta ; five_prime_utr_gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109_five_prime_utr.gtf ; stop_codon_gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109_stop_codon.gtf ; exon /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/exon.tab ; gene_gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109_gene.gtf ; contig_rm /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/contig_rm.tab ; transcript_gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109_transcript.gtf ; cds /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/cds.tab ; contigs_txt /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/contigs.txt ; three_prime_utr_gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109_three_prime_utr.gtf ; gene_end_gtf /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109_gene_end.gtf ; log /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/log.txt ; fasta_pep_lengths /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109.pep.all_lengths.tab ; contigs_txt_rm /opt/rsat-tools/rsat_metazoa/public_html/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/contigs_rm.txt ; fasta_rm_lengths /opt/rsat-tools/rsat_metazoa/data/genomes/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.109.dna_rm.genome_lengths.tab ; Parsed rows per feature type ; cds 527292 ; exon 645197 ; five_prime_utr 64669 ; gene 30108 ; selenocysteine 9 ; start_codon 42579 ; stop_codon 44360 ; three_prime_utr 49184 ; transcript 72689 ; Parsed rows per contig ; Contig Total cds exon five_prime_utr gene selenocysteine start stop three_prime_utr transcript ; 1 207487 71661 91941 9217 4591 0 5864 6119 6878 11216 ; 10 38711 14154 16780 1726 708 0 1104 1164 1296 1779 ; 11 30161 10434 12938 1562 604 0 961 991 1163 1508 ; 12 36455 13625 16224 1423 630 1 932 977 1078 1565 ; 13 27143 9532 11590 1235 621 0 862 901 1019 1383 ; 14 35663 13343 15183 1610 611 0 1060 1106 1263 1487 ; 15 31209 11753 13324 1338 550 0 916 950 1071 1307 ; 16 5714 1743 2141 342 253 0 275 285 258 417 ; 17 29869 11419 13133 1097 513 0 769 805 890 1243 ; 18 27615 10403 11782 1191 460 0 809 850 984 1136 ; 19 27028 10132 11344 1232 500 0 848 886 973 1113 ; 2 145320 50048 65311 6204 3208 0 3923 4090 4447 8089 ; 20 24980 8912 10584 1208 542 0 786 824 910 1214 ; 21 21909 8455 9375 990 337 0 602 641 714 795 ; 22 13198 4832 5610 554 261 0 398 424 485 634 ; 23 18073 6428 7654 907 383 0 565 593 667 876 ; 24 14932 5617 6359 618 272 0 439 464 523 640 ; 25 15138 5184 5936 867 373 0 625 644 718 791 ; 26 19559 7210 8090 985 355 0 654 669 763 833 ; 27 19232 7116 7846 941 400 0 650 695 767 817 ; 28 20812 7640 8590 1004 402 1 705 721 832 917 ; 29 1034 262 306 113 43 0 76 78 74 82 ; 3 124764 43778 56161 5034 2605 0 3343 3445 3822 6576 ; 30 5013 1936 2084 210 77 0 158 164 199 185 ; 31 4558 1478 1761 249 171 0 201 219 200 279 ; 32 227 12 145 8 14 0 2 4 3 39 ; 33 1550 319 401 66 185 0 164 171 46 198 ; 34 13726 5245 5717 555 271 0 444 457 473 564 ; 35 1797 581 747 88 57 0 64 67 71 122 ; 36 832 257 360 33 30 0 28 30 27 67 ; 37 137 9 82 2 12 0 2 2 1 27 ; 38 4649 1887 1995 142 75 1 124 129 144 152 ; 39 972 362 374 43 23 0 39 41 44 46 ; 4 107908 37266 47861 4737 2313 0 3090 3232 3643 5766 ; 5 89337 31853 38990 4125 1745 2 2611 2709 2951 4351 ; 6 54572 19562 24188 2370 973 1 1521 1587 1788 2582 ; 7 68224 26693 30904 2405 900 0 1515 1565 1807 2435 ; 8 53658 20369 23361 2219 831 2 1479 1524 1750 2123 ; 9 41658 14926 18041 2005 772 1 1237 1278 1487 1911 ; JAENSK010000001.1 13 4 4 0 1 0 1 1 1 1 ; JAENSK010000002.1 153 50 57 11 3 0 4 9 10 9 ; JAENSK010000033.1 122 56 56 1 1 0 0 3 2 3 ; JAENSK010000034.1 202 15 87 34 10 0 12 1 12 31 ; JAENSK010000082.1 25 6 8 4 1 0 2 1 1 2 ; JAENSK010000291.1 32 0 21 0 3 0 0 0 0 8 ; JAENSK010000294.1 26 0 20 0 1 0 0 0 0 5 ; JAENSK010000295.1 134 42 44 10 4 0 6 9 10 9 ; JAENSK010000296.1 169 42 84 4 7 0 5 5 4 18 ; JAENSK010000383.1 94 26 26 6 7 0 8 7 6 8 ; JAENSK010000384.1 124 32 39 15 5 0 7 8 8 10 ; JAENSK010000409.1 89 32 33 1 4 0 4 6 3 6 ; JAENSK010000410.1 142 41 56 6 8 0 5 7 6 13 ; JAENSK010000416.1 166 2 128 0 9 0 1 1 0 25 ; JAENSK010000437.1 31 8 8 0 4 0 3 4 0 4 ; JAENSK010000438.1 24 6 6 0 3 0 3 3 0 3 ; JAENSK010000448.1 115 44 56 0 3 0 1 3 0 8 ; JAENSK010000452.1 98 32 36 5 4 0 5 4 5 7 ; JAENSK010000459.1 301 0 204 0 27 0 0 0 0 70 ; JAENSK010000461.1 158 10 88 3 16 0 3 3 2 33 ; JAENSK010000462.1 93 5 55 0 11 0 2 2 0 18 ; JAENSK010000477.1 44 12 13 4 2 0 4 3 2 4 ; JAENSK010000478.1 74 28 30 1 2 0 4 4 0 5 ; JAENSK010000479.1 60 16 23 0 3 0 4 4 3 7 ; JAENSK010000483.1 211 58 74 20 10 0 11 12 11 15 ; JAENSK010000484.1 1178 467 495 40 16 0 33 40 43 44 ; JAENSK010000532.1 114 23 35 6 12 0 7 10 7 14 ; JAENSK010000533.1 170 28 51 7 22 0 14 16 8 24 ; JAENSK010000534.1 114 30 32 8 5 0 7 11 9 12 ; JAENSK010000538.1 21 7 7 0 2 0 1 2 0 2 ; JAENSK010000547.1 119 42 51 11 2 0 3 3 3 4 ; JAENSK010000568.1 51 12 24 2 3 0 1 2 1 6 ; JAENSK010000584.1 293 63 138 13 13 0 8 11 14 33 ; JAENSK010000585.1 210 55 98 7 11 0 6 7 5 21 ; JAENSK010000586.1 129 50 51 5 2 0 5 5 6 5 ; JAENSK010000587.1 280 129 131 8 1 0 1 3 1 6 ; JAENSK010000588.1 18 7 7 0 1 0 0 1 1 1 ; JAENSK010000589.1 15 5 5 1 1 0 0 1 1 1 ; JAENSK010000592.1 592 241 246 18 7 0 15 22 20 23 ; JAENSK010000593.1 61 17 25 2 4 0 1 3 3 6 ; JAENSK010000594.1 53 18 19 3 2 0 2 3 3 3 ; JAENSK010000595.1 152 58 60 4 3 0 5 7 8 7 ; JAENSK010000596.1 27 7 13 1 2 0 1 0 0 3 ; JAENSK010000597.1 27 11 11 1 1 0 1 0 1 1 ; JAENSK010000605.1 144 50 51 4 7 0 7 8 7 10 ; JAENSK010000614.1 21 5 5 2 2 0 2 1 2 2 ; JAENSK010000615.1 131 44 50 7 4 0 9 3 3 11 ; JAENSK010000619.1 58 9 24 3 4 0 2 3 7 6 ; JAENSK010000620.1 85 20 29 5 7 0 6 6 3 9 ; JAENSK010000621.1 102 33 38 4 6 0 3 7 3 8 ; JAENSK010000622.1 104 48 49 2 1 0 1 1 1 1 ; JAENSK010000623.1 155 37 65 17 3 0 7 7 7 12 ; JAENSK010000625.1 110 40 44 7 2 0 4 4 5 4 ; JAENSK010000627.1 89 20 46 1 3 0 3 3 1 12 ; JAENSK010000630.1 22 8 8 0 2 0 1 1 0 2 ; JAENSK010000631.1 30 11 13 3 1 0 0 1 0 1 ; JAENSK010000635.1 93 13 43 7 6 0 2 3 4 15 ; JAENSK010000636.1 24 0 17 0 3 0 0 0 0 4 ; JAENSK010000638.1 106 17 35 12 8 0 8 8 6 12 ; JAENSK010000640.1 54 5 33 1 2 0 0 1 1 11 ; JAENSK010000641.1 45 18 18 1 2 0 0 0 3 3 ; JAENSK010000644.1 73 9 45 0 3 0 1 1 0 14 ; JAENSK010000646.1 57 1 37 0 4 0 1 1 0 13 ; JAENSK010000648.1 12 1 5 0 2 0 1 1 0 2 ; JAENSK010000650.1 60 9 29 7 3 0 1 1 2 8 ; JAENSK010000656.1 32 14 14 1 1 0 0 1 0 1 ; JAENSK010000657.1 14 0 10 0 1 0 0 0 0 3 ; JAENSK010000658.1 12 4 4 0 1 0 1 1 0 1 ; JAENSK010000659.1 6 1 1 0 1 0 1 1 0 1 ; JAENSK010000665.1 22 8 8 1 1 0 1 1 1 1 ; JAENSK010000666.1 23 8 8 0 2 0 2 1 0 2 ; JAENSK010000667.1 7 2 2 0 1 0 1 0 0 1 ; JAENSK010000669.1 12 2 3 2 1 0 1 1 1 1 ; MT 148 14 38 0 37 0 13 9 0 37 ; MU179258.1 507 105 231 23 19 0 11 18 53 47 ; MU179259.1 213 76 80 9 8 0 10 11 6 13 ; MU179260.1 33 4 10 6 1 0 3 3 3 3 ; MU179261.1 462 171 223 12 12 0 7 9 1 27 ; MU179262.1 99 9 54 4 6 0 3 3 0 20 ; MU179263.1 539 173 219 24 16 0 15 24 24 44 ; MU179264.1 232 62 109 10 8 0 8 8 7 20 ; MU179265.1 179 0 145 0 6 0 0 0 0 28 ; MU179266.1 30 7 12 0 3 0 2 2 0 4 ; MU179269.1 12 2 2 0 2 0 2 2 0 2 ; MU179271.1 153 47 55 11 4 0 9 7 8 12 ; MU179272.1 776 112 426 20 47 0 15 14 17 125 ; MU179273.1 870 307 405 27 25 0 19 18 18 51 ; MU179274.1 586 158 256 37 16 0 22 21 22 54 ; MU179276.1 111 18 50 0 13 0 6 6 0 18 ; MU179278.1 719 283 330 17 14 0 14 17 13 31 ; MU179279.1 381 136 147 28 7 0 14 16 13 20 ; W 5676 1755 2280 346 179 0 229 216 294 377 ; Z 71510 25143 31423 3091 1671 0 2060 2141 2199 3782 ; Host name clust-rsat ; Job started 2023-05-24.124649 ; Job done 2023-05-24.201102 ; Seconds 91.32 ; user 91.32 ; system 18.66 ; cuser 24175.04 ; csystem 484.02