; 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