; parse-gtf  -v 2 -i $RSAT/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46.gtf -fasta $RSAT/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46.pep.all.fa -org_name Oryza_sativa.IRGSP-1.0.46 -task all -taxid 39947 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Oryza_sativa.IRGSP-1.0.46/genome/Oryza_sativa.IRGSP-1.0.46_exon.gtf
; Parsed rows per feature type
;	cds          	165166
;	exon         	198053
;	five_prime_utr	45615
;	gene         	38978
;	start_codon  	33170
;	stop_codon   	40418
;	three_prime_utr	51073
;	transcript   	45772
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	88806	24237	28791	6474	5350	4705	5678	7213	6358
;	10           	31933	8322	9990	2388	2184	1763	2174	2602	2510
;	11           	35684	8872	11092	2593	2663	2004	2451	3044	2965
;	12           	34228	8966	10936	2580	2215	1787	2274	2915	2555
;	2            	72118	19483	23496	5366	4296	3787	4573	5986	5131
;	3            	78810	21638	25583	5732	4648	4143	4997	6440	5629
;	4            	54525	14563	17446	3973	3429	2883	3583	4597	4051
;	5            	50469	13640	16256	3860	3070	2720	3231	4066	3626
;	6            	50212	13345	16038	3714	3204	2717	3324	4141	3729
;	7            	46121	12483	14744	3360	2917	2458	3037	3727	3395
;	8            	40919	10724	12888	3060	2636	2268	2758	3498	3087
;	9            	33447	8784	10563	2515	2144	1832	2251	2844	2514
;	Mt           	425	51	95	0	95	48	41	0	95
;	Pt           	548	58	135	0	127	55	46	0	127
; Host name	baobab.eead.csic.es
; Job started	2020-01-16.140411
; Job done	2020-01-16.185412
; Seconds	72.14
;	user	72.14
;	system	4.28
;	cuser	17134.46
;	csystem	239.68