; parse-gtf -v 2 -i $RSAT/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40.gtf -fasta $RSAT/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40.pep.all.fa -org_name Gossypium_raimondii.Graimondii2_0.40 -task all -taxid 29730 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome ; Program version 1.48 ; Input files ; fasta_rm /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40.dna_rm.genome.fa ; gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40.gtf ; fasta /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40.dna.toplevel.fa ; fasta_pep /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40.pep.all.fa ; Output files ; peptidic_sequences /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/peptidic_sequences.fasta ; contigs_txt_rm /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/contigs_rm.txt ; tts_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40_tts.gtf ; gene_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40_gene.gtf ; contig_rm /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/contig_rm.tab ; gene /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/gene.tab ; stop_codon_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40_stop_codon.gtf ; transcript /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/transcript.tab ; gene_start_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40_gene_start.gtf ; gene_end_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40_gene_end.gtf ; cds /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/cds.tab ; three_prime_utr_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40_three_prime_utr.gtf ; log /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/log.txt ; exon /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/exon.tab ; organism /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/organism.tab ; contig /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/contig.tab ; tss_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40_tss.gtf ; stop_codon /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/stop_codon.tab ; start_codon_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40_start_codon.gtf ; five_prime_utr_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40_five_prime_utr.gtf ; transcript_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40_transcript.gtf ; fasta_lengths /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40.dna.toplevel_lengths.tab ; start_codon /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/start_codon.tab ; contigs_txt /var/www/html/rsat/public_html/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/contigs.txt ; fasta_pep_lengths /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40.pep.all_lengths.tab ; fasta_rm_lengths /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40.dna_rm.genome_lengths.tab ; exon_gtf /var/www/html/rsat/data/genomes/Gossypium_raimondii.Graimondii2_0.40/genome/Gossypium_raimondii.Graimondii2_0.40_exon.gtf ; Parsed rows per feature type ; cds 485691 ; exon 486376 ; five_prime_utr 58228 ; gene 38719 ; start_codon 75889 ; stop_codon 36549 ; three_prime_utr 60524 ; transcript 78882 ; Parsed rows per contig ; Contig Total cds exon five_prime_utr gene start stop three_prime_utr transcript ; 1 94328 34388 34437 4292 2841 5533 2618 4488 5731 ; 10 92756 34356 34404 3967 2679 5221 2540 4099 5490 ; 11 98737 36459 36513 4168 3074 5576 2704 4372 5871 ; 12 63173 22892 22942 2895 1959 3763 1823 2980 3919 ; 13 93479 34115 34171 4236 2820 5463 2627 4366 5681 ; 2 94317 34989 35031 4037 2773 5249 2579 4200 5459 ; 3 67363 24697 24728 3011 1932 3895 1929 3106 4065 ; 4 105335 38965 39015 4589 3023 5931 2823 4812 6177 ; 5 90137 32655 32699 4125 2768 5389 2654 4278 5569 ; 6 102212 37936 37996 4425 2843 5739 2718 4614 5941 ; 7 132039 48596 48658 5749 3914 7577 3633 6051 7861 ; 8 111541 40977 41029 5021 3068 6498 3081 5194 6673 ; 9 169985 62886 62969 7456 4699 9665 4621 7710 9979 ; scaffold_102 8 2 2 0 1 1 1 0 1 ; scaffold_107 27 9 9 1 3 1 1 0 3 ; scaffold_108 47 8 8 4 7 7 1 5 7 ; scaffold_111 12 3 3 1 2 0 1 0 2 ; scaffold_112 7 2 2 0 1 0 1 0 1 ; scaffold_114 39 14 14 1 3 2 1 1 3 ; scaffold_115 27 8 8 1 2 2 1 2 3 ; scaffold_116 26 8 8 2 1 2 1 2 2 ; scaffold_119 17 5 5 0 2 1 1 1 2 ; scaffold_122 11 2 2 1 2 1 0 1 2 ; scaffold_126 3 0 1 0 1 0 0 0 1 ; scaffold_127 16 5 5 0 2 1 1 0 2 ; scaffold_129 23 8 8 0 2 2 0 1 2 ; scaffold_135 37 14 14 1 3 2 0 0 3 ; scaffold_14 1728 610 611 80 61 111 51 87 117 ; scaffold_149 28 4 4 4 3 3 3 3 4 ; scaffold_15 765 273 273 31 26 51 24 34 53 ; scaffold_156 5 1 1 0 1 1 0 0 1 ; scaffold_159 11 3 3 1 1 1 1 0 1 ; scaffold_161 61 24 24 3 1 3 0 3 3 ; scaffold_165 32 9 9 3 2 3 0 3 3 ; scaffold_167 11 2 2 1 2 1 0 1 2 ; scaffold_169 42 10 10 4 5 4 2 1 6 ; scaffold_17 185 69 69 8 5 11 4 7 12 ; scaffold_177 29 7 7 3 4 3 0 1 4 ; scaffold_184 8 2 2 0 1 1 1 0 1 ; scaffold_19 27 7 7 1 3 3 2 1 3 ; scaffold_190 21 6 6 1 2 2 1 1 2 ; scaffold_20 62 25 25 0 3 3 1 2 3 ; scaffold_21 34 9 9 2 4 3 1 2 4 ; scaffold_214 81 28 28 4 2 6 3 4 6 ; scaffold_215 85 33 33 3 2 5 1 3 5 ; scaffold_223 8 2 3 0 1 0 1 0 1 ; scaffold_226 21 6 6 0 3 1 2 0 3 ; scaffold_23 86 27 27 3 6 6 5 5 7 ; scaffold_230 26 8 8 2 1 2 1 2 2 ; scaffold_238 17 7 7 0 1 1 0 0 1 ; scaffold_24 18 4 4 2 2 2 0 2 2 ; scaffold_247 8 2 2 0 1 1 1 0 1 ; scaffold_25 24 6 6 2 2 2 1 2 3 ; scaffold_252 18 3 3 1 3 2 2 1 3 ; scaffold_257 10 2 2 0 2 1 0 1 2 ; scaffold_262 12 2 2 0 2 2 2 0 2 ; scaffold_27 12 2 2 2 2 1 1 0 2 ; scaffold_28 22 5 5 1 3 3 2 0 3 ; scaffold_285 7 2 2 0 1 0 0 1 1 ; scaffold_289 27 7 7 2 3 2 1 2 3 ; scaffold_29 135 53 53 5 4 6 2 5 7 ; scaffold_30 9 2 3 0 2 0 0 0 2 ; scaffold_31 29 7 7 3 2 3 1 3 3 ; scaffold_312 31 8 8 2 1 4 4 0 4 ; scaffold_318 12 4 4 0 1 1 1 0 1 ; scaffold_328 10 3 3 0 1 1 0 1 1 ; scaffold_33 44 14 14 1 5 2 2 1 5 ; scaffold_338 12 3 3 0 2 1 1 0 2 ; scaffold_355 22 8 8 1 1 1 1 1 1 ; scaffold_356 11 3 3 1 1 1 0 1 1 ; scaffold_357 25 9 9 1 2 1 1 0 2 ; scaffold_36 42 7 7 4 6 6 3 3 6 ; scaffold_371 27 7 7 1 2 3 3 1 3 ; scaffold_375 8 2 2 0 1 1 1 0 1 ; scaffold_378 15 4 4 0 2 1 0 2 2 ; scaffold_40 12 2 2 0 2 2 2 0 2 ; scaffold_400 16 3 3 2 2 2 0 2 2 ; scaffold_409 19 4 4 2 2 2 2 1 2 ; scaffold_42 17 4 4 1 2 1 2 1 2 ; scaffold_420 22 7 7 1 1 2 0 2 2 ; scaffold_421 65 24 24 3 2 3 1 2 6 ; scaffold_431 30 10 10 2 1 2 1 2 2 ; scaffold_456 49 18 18 1 4 2 2 0 4 ; scaffold_463 17 4 4 1 2 1 1 2 2 ; scaffold_47 32 6 6 1 4 4 4 1 6 ; scaffold_472 50 18 18 1 2 3 2 2 4 ; scaffold_474 8 2 2 0 1 0 1 1 1 ; scaffold_484 12 3 3 0 2 1 0 1 2 ; scaffold_492 15 4 4 1 2 1 1 0 2 ; scaffold_499 19 7 7 1 1 1 0 1 1 ; scaffold_50 18 5 5 1 2 2 0 1 2 ; scaffold_505 11 2 2 0 2 2 1 0 2 ; scaffold_512 45 14 14 2 3 3 3 1 5 ; scaffold_515 14 3 3 0 2 2 1 1 2 ; scaffold_519 37 12 12 2 1 3 2 2 3 ; scaffold_520 133 51 51 9 2 9 0 2 9 ; scaffold_524 26 6 6 3 2 3 1 2 3 ; scaffold_525 6 1 1 0 1 1 1 0 1 ; scaffold_526 7 1 1 1 1 1 0 1 1 ; scaffold_56 14 3 3 2 2 1 0 1 2 ; scaffold_567 27 6 6 2 4 3 2 0 4 ; scaffold_578 9 2 2 0 1 1 1 1 1 ; scaffold_592 11 3 3 1 1 1 0 1 1 ; scaffold_597 20 5 5 1 3 1 0 2 3 ; scaffold_605 13 3 3 1 2 1 1 0 2 ; scaffold_608 6 1 1 0 1 1 1 0 1 ; scaffold_61 31 12 12 0 1 2 1 1 2 ; scaffold_62 10 3 3 0 1 1 1 0 1 ; scaffold_65 23 6 6 1 3 1 2 1 3 ; scaffold_658 19 4 4 2 3 1 0 2 3 ; scaffold_666 8 2 2 0 1 1 1 0 1 ; scaffold_678 24 5 5 3 2 3 1 2 3 ; scaffold_68 50 23 23 0 1 1 0 1 1 ; scaffold_681 12 4 4 0 1 1 1 0 1 ; scaffold_684 23 6 6 2 3 2 1 0 3 ; scaffold_700 7 1 1 0 1 1 1 1 1 ; scaffold_710 5 1 1 0 1 1 0 0 1 ; scaffold_72 7 1 1 1 1 1 0 1 1 ; scaffold_721 7 1 1 1 1 1 0 1 1 ; scaffold_730 7 1 1 1 1 1 0 1 1 ; scaffold_743 11 3 3 0 1 1 1 1 1 ; scaffold_744 10 3 3 0 1 0 1 1 1 ; scaffold_746 6 1 1 0 1 1 1 0 1 ; scaffold_755 24 8 8 0 2 1 2 1 2 ; scaffold_769 12 4 4 1 1 1 0 0 1 ; scaffold_78 35 11 11 2 2 3 1 2 3 ; scaffold_803 10 2 2 1 1 1 1 1 1 ; scaffold_817 13 4 4 0 2 0 1 0 2 ; scaffold_839 12 3 3 1 1 1 1 1 1 ; scaffold_851 8 1 1 1 1 1 1 1 1 ; scaffold_853 15 2 2 2 2 2 1 2 2 ; scaffold_863 11 2 2 1 2 1 1 0 2 ; scaffold_868 7 2 2 0 1 1 0 0 1 ; scaffold_913 6 1 1 0 1 1 1 0 1 ; Host name baobab.eead.csic.es ; Job started 2018-09-15.155058 ; Job done 2018-09-16.001503 ; Seconds 140.39 ; user 140.39 ; system 116.48 ; cuser 26998.65 ; csystem 1992.93