; parse-gtf  -v 2 -i $RSAT/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40.gtf -fasta $RSAT/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40.pep.all.fa -org_name Oryza_nivara.AWHD00000000.40 -task all -taxid 4536 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Oryza_nivara.AWHD00000000.40/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Oryza_nivara.AWHD00000000.40/genome/Oryza_nivara.AWHD00000000.40_exon.gtf
; Parsed rows per feature type
;	cds          	272477
;	exon         	289583
;	five_prime_utr	23271
;	gene         	38741
;	start_codon  	48288
;	stop_codon   	48305
;	three_prime_utr	25246
;	transcript   	50788
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	119780	41688	44221	3517	5426	6937	6943	3817	7231
;	10           	45093	15010	16065	1325	2344	2875	2880	1538	3056
;	11           	47417	15866	16898	1348	2457	3040	3038	1568	3202
;	12           	40567	13577	14555	1316	1998	2549	2542	1345	2685
;	2            	94059	32598	34626	2817	4357	5504	5502	2864	5791
;	3            	97683	33456	35810	2923	4641	5771	5779	3222	6081
;	4            	67087	23338	24679	1876	3152	3941	3940	2015	4146
;	5            	65859	22769	24064	1862	3159	3941	3945	1983	4136
;	6            	65636	22512	23763	1788	3317	4029	4033	1930	4264
;	7            	56591	19101	20269	1725	2844	3565	3558	1806	3723
;	8            	54129	18130	19338	1535	2873	3422	3425	1766	3640
;	9            	42798	14432	15295	1239	2173	2714	2720	1392	2833
; Host name	baobab.eead.csic.es
; Job started	2018-09-22.134833
; Job done	2018-09-22.181553
; Seconds	80.7
;	user	80.7
;	system	19
;	cuser	15308.15
;	csystem	481.01