; parse-gtf -v 2 -i $RSAT/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57.gtf -fasta $RSAT/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57.pep.all.fa -org_name Theobroma_cacao.Theobroma_cacao_20110822.57 -task all -taxid 3641 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome ; Program version 1.48 ; Input files ; gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57.gtf ; fasta_pep /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57.pep.all.fa ; fasta_rm /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57.dna_rm.genome.fa ; fasta /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57.dna.toplevel.fa ; Output files ; organism /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/organism.tab ; peptidic_sequences /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/peptidic_sequences.fasta ; five_prime_utr_gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57_five_prime_utr.gtf ; contig /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/contig.tab ; gene_start_gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57_gene_start.gtf ; three_prime_utr_gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57_three_prime_utr.gtf ; tss_gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57_tss.gtf ; start_codon /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/start_codon.tab ; stop_codon /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/stop_codon.tab ; gene_gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57_gene.gtf ; log /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/log.txt ; transcript_gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57_transcript.gtf ; fasta_rm_lengths /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57.dna_rm.genome_lengths.tab ; gene_end_gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57_gene_end.gtf ; contig_rm /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/contig_rm.tab ; start_codon_gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57_start_codon.gtf ; gene /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/gene.tab ; cds /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/cds.tab ; fasta_pep_lengths /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57.pep.all_lengths.tab ; tts_gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57_tts.gtf ; exon_gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57_exon.gtf ; fasta_lengths /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57.dna.toplevel_lengths.tab ; contigs_txt_rm /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/contigs_rm.txt ; contigs_txt /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/contigs.txt ; exon /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/exon.tab ; stop_codon_gtf /var/www/html/rsat/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/Theobroma_cacao.Theobroma_cacao_20110822.57_stop_codon.gtf ; transcript /var/www/html/rsat/public_html/data/genomes/Theobroma_cacao.Theobroma_cacao_20110822.57/genome/transcript.tab ; Parsed rows per feature type ; cds 264459 ; exon 265055 ; five_prime_utr 41771 ; gene 29653 ; start_codon 43150 ; stop_codon 15747 ; three_prime_utr 41783 ; transcript 44651 ; Parsed rows per contig ; Contig Total cds exon five_prime_utr gene start stop three_prime_utr transcript ; 1 105853 37627 37720 5862 4166 6073 2253 5853 6299 ; 10 44073 15267 15293 2604 1874 2682 962 2616 2775 ; 2 89534 31325 31392 5202 3672 5344 1896 5196 5507 ; 3 83339 29577 29649 4650 3234 4804 1789 4659 4977 ; 4 77824 27314 27360 4484 3159 4620 1658 4477 4752 ; 5 82812 29412 29506 4567 3356 4736 1722 4573 4940 ; 6 63031 22654 22708 3411 2388 3532 1270 3406 3662 ; 7 39065 13184 13214 2426 1880 2490 889 2424 2558 ; 8 55243 19889 19920 2974 2049 3101 1158 2973 3179 ; 9 102523 37407 37486 5339 3632 5522 2052 5350 5735 ; scaffold_101 17 6 6 1 1 1 0 1 1 ; scaffold_107 31 8 8 3 3 3 0 3 3 ; scaffold_11 423 125 125 32 26 35 13 32 35 ; scaffold_110 23 6 6 2 2 2 1 2 2 ; scaffold_112 60 23 23 3 2 3 0 3 3 ; scaffold_115 23 5 6 1 3 2 1 2 3 ; scaffold_116 21 8 8 1 1 1 0 1 1 ; scaffold_117 27 6 6 3 3 2 1 3 3 ; scaffold_12 196 64 64 13 13 13 3 13 13 ; scaffold_120 19 4 4 2 2 2 1 2 2 ; scaffold_126 29 6 6 3 3 3 2 3 3 ; scaffold_13 273 67 67 26 26 26 9 26 26 ; scaffold_133 22 6 6 1 2 2 1 2 2 ; scaffold_138 29 7 7 3 3 3 0 3 3 ; scaffold_147 36 11 11 2 3 2 1 3 3 ; scaffold_15 29 7 7 3 3 2 1 3 3 ; scaffold_160 18 4 4 2 2 2 0 2 2 ; scaffold_161 16 3 3 2 2 2 0 2 2 ; scaffold_174 14 5 5 1 1 1 0 0 1 ; scaffold_176 18 6 6 1 1 1 1 1 1 ; scaffold_180 7 1 1 1 1 1 0 1 1 ; scaffold_184 16 3 3 1 2 2 1 2 2 ; scaffold_186 12 4 4 1 1 0 0 1 1 ; scaffold_187 37 6 6 5 3 5 3 4 5 ; scaffold_195 8 1 1 1 1 1 1 1 1 ; scaffold_196 17 6 6 1 1 1 0 1 1 ; scaffold_198 22 6 6 2 2 1 1 2 2 ; scaffold_203 42 12 12 3 2 2 2 4 5 ; scaffold_214 28 9 9 2 2 2 0 2 2 ; scaffold_219 10 2 2 1 1 1 1 1 1 ; scaffold_230 13 2 2 1 2 2 0 2 2 ; scaffold_237 26 8 8 2 2 2 0 2 2 ; scaffold_245 10 2 2 1 1 1 1 1 1 ; scaffold_248 14 4 4 1 1 1 1 1 1 ; scaffold_250 10 2 2 1 1 1 1 1 1 ; scaffold_254 12 3 3 1 1 1 1 1 1 ; scaffold_255 12 4 4 1 1 0 0 1 1 ; scaffold_26 226 65 65 18 15 18 9 18 18 ; scaffold_262 30 7 7 3 3 3 1 3 3 ; scaffold_264 21 5 5 2 2 2 1 2 2 ; scaffold_266 9 2 2 1 1 1 0 1 1 ; scaffold_273 21 6 6 2 1 2 0 2 2 ; scaffold_28 95 26 26 8 8 8 3 8 8 ; scaffold_281 7 1 1 1 1 1 0 1 1 ; scaffold_299 10 2 2 1 1 1 1 1 1 ; scaffold_304 12 3 3 1 1 1 1 1 1 ; scaffold_309 11 3 3 1 1 1 0 1 1 ; scaffold_31 174 43 43 16 15 16 9 16 16 ; scaffold_311 16 3 3 2 2 2 0 2 2 ; scaffold_318 17 6 6 1 1 1 1 0 1 ; scaffold_32 29 6 6 3 3 3 2 3 3 ; scaffold_324 13 5 5 0 1 0 0 1 1 ; scaffold_327 7 1 1 1 1 1 0 1 1 ; scaffold_332 16 2 3 2 3 0 1 2 3 ; scaffold_36 71 23 23 5 3 5 2 5 5 ; scaffold_368 17 6 6 1 1 1 0 1 1 ; scaffold_37 44 8 8 5 5 5 3 5 5 ; scaffold_377 9 3 3 0 1 0 0 1 1 ; scaffold_382 10 2 2 1 1 1 1 1 1 ; scaffold_39 17 2 3 2 3 2 0 2 3 ; scaffold_392 11 3 3 1 1 1 0 1 1 ; scaffold_397 21 5 5 2 2 2 1 2 2 ; scaffold_401 7 1 1 1 1 1 0 1 1 ; scaffold_417 14 4 4 1 1 1 1 1 1 ; scaffold_43 83 22 23 7 6 8 3 7 7 ; scaffold_455 6 1 1 1 1 0 0 1 1 ; scaffold_51 47 12 12 4 4 4 3 4 4 ; scaffold_514 6 1 1 1 1 0 0 1 1 ; scaffold_522 13 4 4 1 1 0 1 1 1 ; scaffold_534 14 4 4 1 1 1 1 1 1 ; scaffold_543 12 3 3 1 1 1 1 1 1 ; scaffold_545 9 2 2 1 1 1 0 1 1 ; scaffold_55 8 1 1 1 1 1 1 1 1 ; scaffold_58 9 2 2 1 1 1 0 1 1 ; scaffold_68 35 7 7 4 4 4 1 4 4 ; scaffold_703 6 1 1 1 1 0 0 1 1 ; scaffold_73 21 5 5 2 2 2 1 2 2 ; scaffold_812 7 2 2 1 1 0 0 0 1 ; scaffold_815 10 3 3 1 1 0 0 1 1 ; scaffold_82 15 5 5 1 1 1 0 1 1 ; scaffold_83 9 2 2 1 1 1 0 1 1 ; scaffold_85 7 1 1 1 1 1 0 1 1 ; scaffold_88 16 3 3 2 2 2 0 2 2 ; scaffold_91 11 3 3 1 1 1 0 1 1 ; scaffold_93 40 15 15 2 1 2 1 2 2 ; scaffold_94 9 2 2 1 1 1 0 1 1 ; scaffold_96 15 5 5 1 1 1 0 1 1 ; scaffold_97 9 2 2 1 1 1 0 1 1 ; Host name baobab ; Job started 2023-12-07.121710 ; Job done 2023-12-07.160044 ; Seconds 56.03 ; user 56.03 ; system 2.96 ; cuser 13211.79 ; csystem 181.24