; parse-gtf -v 2 -i $RSAT/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF.gtf -fasta $RSAT/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF.pep.all.fa -org_name Fagus_sylvatica.Bhaga_Chr.v2.SBiKF -task all -taxid 28930 -gtf_source SBiKF -o $RSAT/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome ; Program version 1.48 ; Input files ; fasta_pep /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF.pep.all.fa ; gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF.gtf ; fasta /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF.dna.toplevel.fa ; fasta_rm /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF.dna_rm.genome.fa ; Output files ; fasta_rm_lengths /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF.dna_rm.genome_lengths.tab ; exon /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/exon.tab ; transcript_gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF_transcript.gtf ; log /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/log.txt ; transcript /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/transcript.tab ; stop_codon_gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF_stop_codon.gtf ; exon_gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF_exon.gtf ; stop_codon /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/stop_codon.tab ; gene /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/gene.tab ; peptidic_sequences /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/peptidic_sequences.fasta ; contigs_txt_rm /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/contigs_rm.txt ; contigs_txt /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/contigs.txt ; cds /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/cds.tab ; gene_end_gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF_gene_end.gtf ; organism /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/organism.tab ; tts_gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF_tts.gtf ; contig_rm /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/contig_rm.tab ; gene_gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF_gene.gtf ; gene_start_gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF_gene_start.gtf ; fasta_lengths /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF.dna.toplevel_lengths.tab ; five_prime_utr_gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF_five_prime_utr.gtf ; tss_gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF_tss.gtf ; start_codon /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/start_codon.tab ; fasta_pep_lengths /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF.pep.all_lengths.tab ; start_codon_gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF_start_codon.gtf ; contig /var/www/html/rsat/public_html/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/contig.tab ; three_prime_utr_gtf /var/www/html/rsat/data/genomes/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF/genome/Fagus_sylvatica.Bhaga_Chr.v2.SBiKF_three_prime_utr.gtf ; Parsed rows per feature type ; 5 ; cds 297959 ; exon 317857 ; gene 62179 ; intron 233287 ; mrna 64672 ; start_codon 64672 ; stop_codon 64672 ; transcription_end_site 64672 ; transcription_start_site 64672 ; Parsed rows per contig ; Contig Total cds exon gene intron mrna start stop transcription_end_site transcription_start_site ; # FASTA deflines: Bhaga_2, Bhaga_Unplaced_3096, Bhaga_Unplaced_2332, Bhaga_12, Bhaga_Unplaced_5965, Bhaga_Unplaced_5381, Bhaga_Unplaced_565, Bhaga_Unplaced_6180, Bhaga_Unplaced_6042, Bhaga_Unplaced_1969, Bhaga_Unplaced_701, Bhaga_8, Bhaga_Unplaced_3901, Bhaga_Unplaced_4729, Bhaga_Unplaced_6538, Bhaga_Unplaced_255, Bhaga_Unplaced_5639, Bhaga_Unplaced_2098, Bhaga_Unplaced_4346, Bhaga_Unplaced_2901, Bhaga_Unplaced_5343, Bhaga_Unplaced_6670, Bhaga_Unplaced_3039, Bhaga_5, Bhaga_Unplaced_5815, Bhaga_Unplaced_6399, Bhaga_Unplaced_5500, Bhaga_Unplaced_6231, Bhaga_7, Bhaga_Unplaced_1997, Bhaga_Unplaced_4105, Bhaga_Unplaced_5397, Bhaga_Unplaced_24, Bhaga_Unplaced_330, Bhaga_Unplaced_6451, Bhaga_Unplaced_5524, Bhaga_Unplaced_3123, Bhaga_1, Bhaga_Unplaced_6586, Bhaga_Unplaced_5494, Bhaga_Unplaced_801, Bhaga_Unplaced_6325, Bhaga_Unplaced_621, Bhaga_Unplaced_3042, Bhaga_Unplaced_1709, Bhaga_Unplaced_1180, Bhaga_Unplaced_6475, Bhaga_Unplaced_6134, Bhaga_Unplaced_6349, Bhaga_Unplaced_3071, Bhaga_Unplaced_546, Bhaga_Unplaced_1597, Bhaga_Unplaced_3442, Bhaga_Unplaced_4916, Bhaga_Unplaced_3299, Bhaga_9, Bhaga_Unplaced_6597, Bhaga_Unplaced_4025, Bhaga_Unplaced_3606, Bhaga_Unplaced_5803, Bhaga_Unplaced_1952, Bhaga_Unplaced_3381, Bhaga_Unplaced_6370, Bhaga_6, Bhaga_Unplaced_1192, Bhaga_Unplaced_6668, Bhaga_Unplaced_5859, Bhaga_Unplaced_916, Bhaga_Unplaced_6217, Bhaga_Unplaced_4287, Bhaga_Unplaced_1700, Bhaga_Unplaced_6069, Bhaga_Unplaced_5994, Bhaga_Unplaced_3545, Bhaga_Unplaced_6685, Bhaga_Unplaced_2260, Bhaga_Unplaced_3337, Bhaga_Unplaced_5475, Bhaga_Unplaced_1115, Bhaga_Unplaced_3542, Bhaga_Unplaced_6356, Bhaga_Unplaced_5793, Bhaga_Unplaced_6306, Bhaga_Unplaced_1784, Bhaga_11, Bhaga_Unplaced_6611, Bhaga_Unplaced_317, Bhaga_Unplaced_2950, Bhaga_Unplaced_4853, Bhaga_Unplaced_2547, Bhaga_4, Bhaga_Unplaced_6045, Bhaga_Unplaced_5910, Bhaga_10, Bhaga_Unplaced_4617, Bhaga_Unplaced_2436, Bhaga_Unplaced_6478, Bhaga_Unplaced_3676, Bhaga_Unplaced_2887, Bhaga_3, Bhaga_Unplaced_4066, Bhaga_Unplaced_6137, Bhaga_Unplaced_2852, Bhaga_Unplaced_5927, Bhaga_Unplaced_6329, Bhaga_Unplaced_5400, Bhaga_Unplaced_827 1 1 0 0 0 0 0 0 0 0 0 ; # File created on: 2020/11/16_06:25:26 1 1 0 0 0 0 0 0 0 0 0 ; # Number of FASTA deflines: 107 1 1 0 0 0 0 0 0 0 0 0 ; # gff generated with Blast2GO 1 1 0 0 0 0 0 0 0 0 0 ; ##gff-version 3 1 1 0 0 0 0 0 0 0 0 0 ; Bhaga_1 137039 0 32014 34665 7494 24301 7713 7713 7713 7713 7713 ; Bhaga_10 89914 0 21885 23315 4413 17281 4604 4604 4604 4604 4604 ; Bhaga_11 79942 0 19411 20646 3958 15282 4129 4129 4129 4129 4129 ; Bhaga_12 68301 0 16649 17673 3366 13158 3491 3491 3491 3491 3491 ; Bhaga_2 123901 0 29760 31897 6312 23217 6543 6543 6543 6543 6543 ; Bhaga_3 109881 0 26658 28374 5471 20978 5680 5680 5680 5680 5680 ; Bhaga_4 117422 0 28500 30333 5753 22416 6084 6084 6084 6084 6084 ; Bhaga_5 103006 0 24489 26154 5414 18874 5615 5615 5615 5615 5615 ; Bhaga_6 108179 0 26653 28333 5140 21303 5350 5350 5350 5350 5350 ; Bhaga_7 96642 0 23417 24893 4847 18400 5017 5017 5017 5017 5017 ; Bhaga_8 96704 0 23546 24974 4762 18577 4969 4969 4969 4969 4969 ; Bhaga_9 92526 0 22291 23779 4697 17424 4867 4867 4867 4867 4867 ; Bhaga_Unplaced_1115 85 0 18 20 5 12 6 6 6 6 6 ; Bhaga_Unplaced_1180 450 0 103 111 25 76 27 27 27 27 27 ; Bhaga_Unplaced_1192 392 0 101 108 14 84 17 17 17 17 17 ; Bhaga_Unplaced_1597 510 0 126 134 24 101 25 25 25 25 25 ; Bhaga_Unplaced_1700 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_1709 195 0 47 48 9 36 11 11 11 11 11 ; Bhaga_Unplaced_1784 261 0 63 68 11 49 14 14 14 14 14 ; Bhaga_Unplaced_1952 836 0 214 224 36 177 37 37 37 37 37 ; Bhaga_Unplaced_1969 61 0 15 16 3 12 3 3 3 3 3 ; Bhaga_Unplaced_1997 170 0 37 41 11 26 11 11 11 11 11 ; Bhaga_Unplaced_2098 397 0 92 105 20 70 22 22 22 22 22 ; Bhaga_Unplaced_2260 91 0 27 27 2 25 2 2 2 2 2 ; Bhaga_Unplaced_2332 428 0 99 100 26 73 26 26 26 26 26 ; Bhaga_Unplaced_24 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_2436 31 0 7 7 2 5 2 2 2 2 2 ; Bhaga_Unplaced_2547 26 0 7 7 1 6 1 1 1 1 1 ; Bhaga_Unplaced_255 409 0 103 108 19 84 19 19 19 19 19 ; Bhaga_Unplaced_2852 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_2887 49 0 13 13 2 11 2 2 2 2 2 ; Bhaga_Unplaced_2901 200 0 47 51 11 36 11 11 11 11 11 ; Bhaga_Unplaced_2950 28 0 6 6 2 4 2 2 2 2 2 ; Bhaga_Unplaced_3039 14 0 2 5 1 1 1 1 1 1 1 ; Bhaga_Unplaced_3042 46 0 12 12 2 10 2 2 2 2 2 ; Bhaga_Unplaced_3071 101 0 23 25 6 17 6 6 6 6 6 ; Bhaga_Unplaced_3096 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_3123 100 0 23 23 3 16 7 7 7 7 7 ; Bhaga_Unplaced_317 161 0 32 37 12 20 12 12 12 12 12 ; Bhaga_Unplaced_3299 8 0 1 1 1 0 1 1 1 1 1 ; Bhaga_Unplaced_330 101 0 29 29 2 26 3 3 3 3 3 ; Bhaga_Unplaced_3337 60 0 13 14 4 9 4 4 4 4 4 ; Bhaga_Unplaced_3381 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_3442 96 0 19 23 7 12 7 7 7 7 7 ; Bhaga_Unplaced_3542 82 0 19 20 4 14 5 5 5 5 5 ; Bhaga_Unplaced_3545 63 0 16 16 3 13 3 3 3 3 3 ; Bhaga_Unplaced_3606 449 0 111 116 19 88 23 23 23 23 23 ; Bhaga_Unplaced_3676 64 0 16 17 3 13 3 3 3 3 3 ; Bhaga_Unplaced_3901 186 0 48 48 6 39 9 9 9 9 9 ; Bhaga_Unplaced_4025 75 0 18 19 4 14 4 4 4 4 4 ; Bhaga_Unplaced_4066 8 0 1 1 1 0 1 1 1 1 1 ; Bhaga_Unplaced_4105 8 0 1 1 1 0 1 1 1 1 1 ; Bhaga_Unplaced_4287 22 0 4 4 2 2 2 2 2 2 2 ; Bhaga_Unplaced_4346 19 0 3 3 2 1 2 2 2 2 2 ; Bhaga_Unplaced_4617 74 0 20 20 2 17 3 3 3 3 3 ; Bhaga_Unplaced_4729 49 0 11 12 3 8 3 3 3 3 3 ; Bhaga_Unplaced_4853 116 0 29 29 5 23 6 6 6 6 6 ; Bhaga_Unplaced_4916 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_5343 124 0 29 29 5 21 8 8 8 8 8 ; Bhaga_Unplaced_5381 165 0 44 44 5 37 7 7 7 7 7 ; Bhaga_Unplaced_5397 23 0 6 6 1 5 1 1 1 1 1 ; Bhaga_Unplaced_5400 91 0 23 25 4 19 4 4 4 4 4 ; Bhaga_Unplaced_546 189 0 45 46 9 34 11 11 11 11 11 ; Bhaga_Unplaced_5475 71 0 17 18 3 13 4 4 4 4 4 ; Bhaga_Unplaced_5494 12 0 2 3 1 1 1 1 1 1 1 ; Bhaga_Unplaced_5500 38 0 9 10 2 7 2 2 2 2 2 ; Bhaga_Unplaced_5524 8 0 1 1 1 0 1 1 1 1 1 ; Bhaga_Unplaced_5639 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_565 743 0 177 190 35 136 41 41 41 41 41 ; Bhaga_Unplaced_5793 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_5803 83 0 20 23 4 16 4 4 4 4 4 ; Bhaga_Unplaced_5815 20 0 5 5 1 4 1 1 1 1 1 ; Bhaga_Unplaced_5859 107 0 26 26 5 20 6 6 6 6 6 ; Bhaga_Unplaced_5910 63 0 16 16 3 13 3 3 3 3 3 ; Bhaga_Unplaced_5927 22 0 5 7 1 4 1 1 1 1 1 ; Bhaga_Unplaced_5965 107 0 29 29 4 25 4 4 4 4 4 ; Bhaga_Unplaced_5994 50 0 13 14 2 11 2 2 2 2 2 ; Bhaga_Unplaced_6042 20 0 5 5 1 4 1 1 1 1 1 ; Bhaga_Unplaced_6045 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_6069 22 0 4 4 2 2 2 2 2 2 2 ; Bhaga_Unplaced_6134 61 0 15 16 3 12 3 3 3 3 3 ; Bhaga_Unplaced_6137 14 0 3 3 1 2 1 1 1 1 1 ; Bhaga_Unplaced_6180 110 0 25 25 7 18 7 7 7 7 7 ; Bhaga_Unplaced_621 960 0 229 238 52 176 53 53 53 53 53 ; Bhaga_Unplaced_6217 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_6231 61 0 14 14 3 10 4 4 4 4 4 ; Bhaga_Unplaced_6306 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_6325 45 0 10 10 3 7 3 3 3 3 3 ; Bhaga_Unplaced_6329 89 0 23 23 4 19 4 4 4 4 4 ; Bhaga_Unplaced_6349 53 0 11 11 4 7 4 4 4 4 4 ; Bhaga_Unplaced_6356 108 0 26 27 5 20 6 6 6 6 6 ; Bhaga_Unplaced_6370 155 0 38 38 5 29 9 9 9 9 9 ; Bhaga_Unplaced_6399 36 0 10 11 1 9 1 1 1 1 1 ; Bhaga_Unplaced_6451 52 0 14 14 2 12 2 2 2 2 2 ; Bhaga_Unplaced_6475 90 0 25 25 3 22 3 3 3 3 3 ; Bhaga_Unplaced_6478 26 0 7 7 1 6 1 1 1 1 1 ; Bhaga_Unplaced_6538 91 0 21 21 4 15 6 6 6 6 6 ; Bhaga_Unplaced_6586 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_6597 11 0 2 2 1 1 1 1 1 1 1 ; Bhaga_Unplaced_6611 46 0 12 12 2 10 2 2 2 2 2 ; Bhaga_Unplaced_6668 130 0 31 31 5 23 8 8 8 8 8 ; Bhaga_Unplaced_6670 14 0 3 3 1 2 1 1 1 1 1 ; Bhaga_Unplaced_6685 23 0 6 6 1 5 1 1 1 1 1 ; Bhaga_Unplaced_701 8 0 1 1 1 0 1 1 1 1 1 ; Bhaga_Unplaced_801 63 0 16 16 3 13 3 3 3 3 3 ; Bhaga_Unplaced_827 246 0 50 52 18 31 19 19 19 19 19 ; Bhaga_Unplaced_916 82 0 18 21 5 13 5 5 5 5 5 ; Host name baobab ; Job started 2023-08-21.151301 ; Job done 2023-08-21.215157 ; Seconds 64.67 ; user 64.67 ; system 3.81 ; cuser 23652.96 ; csystem 277.39