; parse-gtf  -v 2 -i $RSAT/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40.gtf -fasta $RSAT/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40.pep.all.fa -org_name Oryza_indica.ASM465v1.40 -task all -taxid 39946 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Oryza_indica.ASM465v1.40/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Oryza_indica.ASM465v1.40/genome/Oryza_indica.ASM465v1.40_exon.gtf
; Parsed rows per feature type
;	cds          	170487
;	exon         	219474
;	gene         	89723
;	start_codon  	40745
;	stop_codon   	40745
;	transcript   	89723
; Parsed rows per contig
;	Contig       	Total	cds	exon	gene	start	stop	transcript
;	1            	86897	23904	29879	11265	5292	5292	11265
;	10           	34672	8605	11511	5092	2186	2186	5092
;	11           	35631	8692	11789	5335	2240	2240	5335
;	12           	36053	9126	12217	5223	2132	2132	5223
;	2            	69293	19277	24098	8890	4069	4069	8890
;	3            	78324	21673	27121	10106	4659	4659	10106
;	4            	56959	15002	19449	7849	3405	3405	7849
;	5            	51679	13569	17660	7158	3067	3067	7158
;	6            	52749	13573	17890	7480	3163	3163	7480
;	7            	46230	12116	15714	6399	2801	2801	6399
;	8            	45570	11309	15269	6728	2768	2768	6728
;	9            	34298	8839	11585	4841	2096	2096	4841
;	AAAA02035458.1	6	1	1	1	1	1	1
;	AAAA02035470.1	134	43	43	12	12	12	12
;	AAAA02035471.1	20	6	6	2	2	2	2
;	AAAA02035472.1	14	3	3	2	2	2	2
;	AAAA02035578.1	108	40	40	7	7	7	7
;	AAAA02035589.1	40	8	8	6	6	6	6
;	AAAA02035594.1	38	11	11	4	4	4	4
;	AAAA02035612.1	20	6	6	2	2	2	2
;	AAAA02035659.1	14	3	3	2	2	2	2
;	AAAA02035660.1	32	8	8	4	4	4	4
;	AAAA02035672.1	6	1	1	1	1	1	1
;	AAAA02035682.1	58	15	15	7	7	7	7
;	AAAA02035683.1	52	18	18	4	4	4	4
;	AAAA02035694.1	8	2	2	1	1	1	1
;	AAAA02035704.1	22	7	7	2	2	2	2
;	AAAA02035705.1	10	3	3	1	1	1	1
;	AAAA02035746.1	20	4	4	3	3	3	3
;	AAAA02035747.1	50	19	19	3	3	3	3
;	AAAA02035821.1	18	5	5	2	2	2	2
;	AAAA02035822.1	38	13	13	3	3	3	3
;	AAAA02035823.1	38	13	13	3	3	3	3
;	AAAA02035839.1	14	5	5	1	1	1	1
;	AAAA02035845.1	40	14	14	3	3	3	3
;	AAAA02035850.1	12	4	4	1	1	1	1
;	AAAA02035863.1	56	20	20	4	4	4	4
;	AAAA02035866.1	12	2	2	2	2	2	2
;	AAAA02035869.1	14	3	3	2	2	2	2
;	AAAA02035894.1	18	3	3	3	3	3	3
;	AAAA02035924.1	50	15	15	5	5	5	5
;	AAAA02035981.1	32	10	10	3	3	3	3
;	AAAA02035993.1	28	6	6	4	4	4	4
;	AAAA02036009.1	20	6	6	2	2	2	2
;	AAAA02036011.1	8	2	2	1	1	1	1
;	AAAA02036020.1	22	5	5	3	3	3	3
;	AAAA02036049.1	8	2	2	1	1	1	1
;	AAAA02036132.1	20	8	8	1	1	1	1
;	AAAA02036135.1	8	2	2	1	1	1	1
;	AAAA02036143.1	38	13	13	3	3	3	3
;	AAAA02036153.1	30	13	13	1	1	1	1
;	AAAA02036172.1	14	3	3	2	2	2	2
;	AAAA02036180.1	30	7	7	4	4	4	4
;	AAAA02036181.1	28	10	10	2	2	2	2
;	AAAA02036185.1	28	10	10	2	2	2	2
;	AAAA02036229.1	6	1	1	1	1	1	1
;	AAAA02036236.1	21	5	6	3	2	2	3
;	AAAA02036261.1	6	1	1	1	1	1	1
;	AAAA02036283.1	52	20	20	3	3	3	3
;	AAAA02036298.1	8	2	2	1	1	1	1
;	AAAA02036300.1	34	7	7	5	5	5	5
;	AAAA02036314.1	19	4	5	3	2	2	3
;	AAAA02036315.1	16	4	4	2	2	2	2
;	AAAA02036352.1	34	7	7	5	5	5	5
;	AAAA02036366.1	48	18	18	3	3	3	3
;	AAAA02036368.1	12	4	4	1	1	1	1
;	AAAA02036386.1	8	2	2	1	1	1	1
;	AAAA02036388.1	8	2	2	1	1	1	1
;	AAAA02036392.1	6	1	1	1	1	1	1
;	AAAA02036401.1	14	3	3	2	2	2	2
;	AAAA02036407.1	16	4	4	2	2	2	2
;	AAAA02036451.1	8	2	2	1	1	1	1
;	AAAA02036459.1	30	7	7	4	4	4	4
;	AAAA02036494.1	6	1	1	1	1	1	1
;	AAAA02036498.1	14	5	5	1	1	1	1
;	AAAA02036507.1	8	2	2	1	1	1	1
;	AAAA02036508.1	12	2	2	2	2	2	2
;	AAAA02036513.1	20	6	6	2	2	2	2
;	AAAA02036514.1	8	2	2	1	1	1	1
;	AAAA02036519.1	8	2	2	1	1	1	1
;	AAAA02036531.1	12	4	4	1	1	1	1
;	AAAA02036544.1	6	1	1	1	1	1	1
;	AAAA02036599.1	12	4	4	1	1	1	1
;	AAAA02036602.1	6	1	1	1	1	1	1
;	AAAA02036617.1	16	4	4	2	2	2	2
;	AAAA02036631.1	10	3	3	1	1	1	1
;	AAAA02036632.1	8	2	2	1	1	1	1
;	AAAA02036649.1	12	2	2	2	2	2	2
;	AAAA02036657.1	8	2	2	1	1	1	1
;	AAAA02036675.1	6	1	1	1	1	1	1
;	AAAA02036682.1	12	2	2	2	2	2	2
;	AAAA02036692.1	14	3	3	2	2	2	2
;	AAAA02036693.1	6	1	1	1	1	1	1
;	AAAA02036701.1	28	12	12	1	1	1	1
;	AAAA02036702.1	8	2	2	1	1	1	1
;	AAAA02036705.1	8	2	2	1	1	1	1
;	AAAA02036719.1	18	3	3	3	3	3	3
;	AAAA02036741.1	8	2	2	1	1	1	1
;	AAAA02036761.1	6	1	1	1	1	1	1
;	AAAA02036811.1	20	4	4	3	3	3	3
;	AAAA02036812.1	10	3	3	1	1	1	1
;	AAAA02036813.1	12	4	4	1	1	1	1
;	AAAA02036828.1	34	13	13	2	2	2	2
;	AAAA02036851.1	117	0	39	39	0	0	39
;	AAAA02036879.1	6	1	1	1	1	1	1
;	AAAA02036888.1	8	2	2	1	1	1	1
;	AAAA02036900.1	16	6	6	1	1	1	1
;	AAAA02036907.1	6	1	1	1	1	1	1
;	AAAA02036929.1	8	2	2	1	1	1	1
;	AAAA02036935.1	8	2	2	1	1	1	1
;	AAAA02036945.1	6	1	1	1	1	1	1
;	AAAA02036946.1	10	3	3	1	1	1	1
;	AAAA02036979.1	6	1	1	1	1	1	1
;	AAAA02036980.1	6	1	1	1	1	1	1
;	AAAA02037002.1	20	6	6	2	2	2	2
;	AAAA02037005.1	10	3	3	1	1	1	1
;	AAAA02037006.1	9	1	2	2	1	1	2
;	AAAA02037017.1	8	2	2	1	1	1	1
;	AAAA02037021.1	6	1	1	1	1	1	1
;	AAAA02037029.1	16	6	6	1	1	1	1
;	AAAA02037039.1	6	1	1	1	1	1	1
;	AAAA02037042.1	6	1	1	1	1	1	1
;	AAAA02037043.1	12	4	4	1	1	1	1
;	AAAA02037077.1	6	1	1	1	1	1	1
;	AAAA02037079.1	46	17	17	3	3	3	3
;	AAAA02037087.1	6	1	1	1	1	1	1
;	AAAA02037088.1	9	0	3	3	0	0	3
;	AAAA02037096.1	8	2	2	1	1	1	1
;	AAAA02037097.1	12	2	2	2	2	2	2
;	AAAA02037115.1	10	3	3	1	1	1	1
;	AAAA02037135.1	8	2	2	1	1	1	1
;	AAAA02037136.1	6	1	1	1	1	1	1
;	AAAA02037149.1	14	5	5	1	1	1	1
;	AAAA02037227.1	8	2	2	1	1	1	1
;	AAAA02037265.1	6	1	1	1	1	1	1
;	AAAA02037303.1	24	8	8	2	2	2	2
;	AAAA02037305.1	9	0	3	3	0	0	3
;	AAAA02037319.1	12	2	2	2	2	2	2
;	AAAA02037329.1	6	1	1	1	1	1	1
;	AAAA02037339.1	10	3	3	1	1	1	1
;	AAAA02037344.1	14	3	3	2	2	2	2
;	AAAA02037345.1	12	4	4	1	1	1	1
;	AAAA02037356.1	6	1	1	1	1	1	1
;	AAAA02037416.1	6	1	1	1	1	1	1
;	AAAA02037451.1	6	0	2	2	0	0	2
;	AAAA02037454.1	96	0	32	32	0	0	32
;	AAAA02037480.1	84	0	28	28	0	0	28
;	AAAA02037512.1	8	2	2	1	1	1	1
;	AAAA02037541.1	12	4	4	1	1	1	1
;	AAAA02037562.1	6	1	1	1	1	1	1
;	AAAA02037563.1	24	8	8	2	2	2	2
;	AAAA02037564.1	6	1	1	1	1	1	1
;	AAAA02037565.1	6	1	1	1	1	1	1
;	AAAA02037588.1	8	2	2	1	1	1	1
;	AAAA02037597.1	6	1	1	1	1	1	1
;	AAAA02037602.1	8	2	2	1	1	1	1
;	AAAA02037624.1	6	1	1	1	1	1	1
;	AAAA02037638.1	20	3	5	4	2	2	4
;	AAAA02037639.1	8	2	2	1	1	1	1
;	AAAA02037644.1	18	3	3	3	3	3	3
;	AAAA02037682.1	16	4	4	2	2	2	2
;	AAAA02037730.1	6	1	1	1	1	1	1
;	AAAA02037773.1	14	3	3	2	2	2	2
;	AAAA02037820.1	12	2	2	2	2	2	2
;	AAAA02037822.1	12	4	4	1	1	1	1
;	AAAA02037857.1	6	1	1	1	1	1	1
;	AAAA02037865.1	34	13	13	2	2	2	2
;	AAAA02037874.1	12	2	2	2	2	2	2
;	AAAA02037890.1	6	1	1	1	1	1	1
;	AAAA02037902.1	6	1	1	1	1	1	1
;	AAAA02037903.1	6	1	1	1	1	1	1
;	AAAA02037931.1	6	0	2	2	0	0	2
;	AAAA02037933.1	20	4	4	3	3	3	3
;	AAAA02037937.1	6	1	1	1	1	1	1
;	AAAA02037946.1	6	1	1	1	1	1	1
;	AAAA02037950.1	6	1	1	1	1	1	1
;	AAAA02037975.1	6	1	1	1	1	1	1
;	AAAA02037981.1	22	5	5	3	3	3	3
;	AAAA02038008.1	3	0	1	1	0	0	1
;	AAAA02038017.1	6	1	1	1	1	1	1
;	AAAA02038034.1	6	1	1	1	1	1	1
;	AAAA02038059.1	12	4	4	1	1	1	1
;	AAAA02038077.1	6	1	1	1	1	1	1
;	AAAA02038080.1	6	1	1	1	1	1	1
;	AAAA02038098.1	28	6	6	4	4	4	4
;	AAAA02038115.1	6	1	1	1	1	1	1
;	AAAA02038130.1	3	0	1	1	0	0	1
;	AAAA02038140.1	3	0	1	1	0	0	1
;	AAAA02038159.1	6	1	1	1	1	1	1
;	AAAA02038245.1	18	3	3	3	3	3	3
;	AAAA02038266.1	6	1	1	1	1	1	1
;	AAAA02038269.1	6	1	1	1	1	1	1
;	AAAA02038319.1	14	3	3	2	2	2	2
;	AAAA02038326.1	18	3	3	3	3	3	3
;	AAAA02038337.1	26	7	7	3	3	3	3
;	AAAA02038350.1	12	2	2	2	2	2	2
;	AAAA02038353.1	6	1	1	1	1	1	1
;	AAAA02038364.1	6	1	1	1	1	1	1
;	AAAA02038379.1	6	1	1	1	1	1	1
;	AAAA02038413.1	6	1	1	1	1	1	1
;	AAAA02038414.1	14	3	3	2	2	2	2
;	AAAA02038419.1	8	2	2	1	1	1	1
;	AAAA02038440.1	6	1	1	1	1	1	1
;	AAAA02038481.1	10	3	3	1	1	1	1
;	AAAA02038502.1	12	2	2	2	2	2	2
;	AAAA02038529.1	6	1	1	1	1	1	1
;	AAAA02038537.1	6	1	1	1	1	1	1
;	AAAA02038538.1	6	1	1	1	1	1	1
;	AAAA02038540.1	3	0	1	1	0	0	1
;	AAAA02038559.1	12	2	2	2	2	2	2
;	AAAA02038571.1	6	1	1	1	1	1	1
;	AAAA02038573.1	6	1	1	1	1	1	1
;	AAAA02038574.1	6	1	1	1	1	1	1
;	AAAA02038597.1	8	2	2	1	1	1	1
;	AAAA02038623.1	6	1	1	1	1	1	1
;	AAAA02038624.1	12	2	2	2	2	2	2
;	AAAA02038625.1	20	6	6	2	2	2	2
;	AAAA02038638.1	24	4	4	4	4	4	4
;	AAAA02038657.1	20	4	4	3	3	3	3
;	AAAA02038677.1	6	1	1	1	1	1	1
;	AAAA02038682.1	6	1	1	1	1	1	1
;	AAAA02038692.1	8	2	2	1	1	1	1
;	AAAA02038711.1	8	2	2	1	1	1	1
;	AAAA02038714.1	6	1	1	1	1	1	1
;	AAAA02038721.1	6	1	1	1	1	1	1
;	AAAA02038744.1	18	3	3	3	3	3	3
;	AAAA02038766.1	26	9	9	2	2	2	2
;	AAAA02038820.1	6	1	1	1	1	1	1
;	AAAA02038848.1	6	1	1	1	1	1	1
;	AAAA02038854.1	8	2	2	1	1	1	1
;	AAAA02038895.1	18	3	3	3	3	3	3
;	AAAA02038899.1	20	4	4	3	3	3	3
;	AAAA02038909.1	12	2	2	2	2	2	2
;	AAAA02038910.1	8	2	2	1	1	1	1
;	AAAA02038931.1	6	1	1	1	1	1	1
;	AAAA02038956.1	6	1	1	1	1	1	1
;	AAAA02038971.1	22	5	5	3	3	3	3
;	AAAA02038974.1	6	1	1	1	1	1	1
;	AAAA02038975.1	3	0	1	1	0	0	1
;	AAAA02038993.1	30	9	9	3	3	3	3
;	AAAA02039059.1	22	5	5	3	3	3	3
;	AAAA02039062.1	6	1	1	1	1	1	1
;	AAAA02039085.1	6	1	1	1	1	1	1
;	AAAA02039097.1	6	1	1	1	1	1	1
;	AAAA02039127.1	6	1	1	1	1	1	1
;	AAAA02039134.1	6	1	1	1	1	1	1
;	AAAA02039143.1	20	6	6	2	2	2	2
;	AAAA02039144.1	27	4	5	5	4	4	5
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; Host name	baobab.eead.csic.es
; Job started	2018-09-21.231127
; Job done	2018-09-22.061859
; Seconds	84.57
;	user	84.57
;	system	7.06
;	cuser	25369.5
;	csystem	289.87