; parse-gtf  -v 2 -i $RSAT/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40.gtf -fasta $RSAT/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40.pep.all.fa -org_name Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40 -task all -taxid 4558 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40/genome/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.40_exon.gtf
; Parsed rows per feature type
;	cds          	239842
;	exon         	241315
;	five_prime_utr	34257
;	gene         	35479
;	start_codon  	46775
;	stop_codon   	22628
;	three_prime_utr	36391
;	transcript   	48471
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	123604	42741	42905	5953	5872	7934	3773	6300	8126
;	10           	59942	20414	20501	2884	3026	4005	1898	3104	4110
;	2            	90856	30996	31123	4376	4524	6059	2920	4639	6219
;	3            	100867	35104	35217	4734	4775	6411	3038	5032	6556
;	4            	80403	27607	27769	3882	3932	5209	2537	4095	5372
;	5            	42769	13755	13813	2247	2488	3190	1606	2383	3287
;	6            	62477	21356	21479	3016	3061	4117	2001	3205	4242
;	7            	45518	14978	15043	2363	2431	3249	1604	2528	3322
;	8            	40721	13712	13760	1996	2069	2791	1422	2113	2858
;	9            	56482	18896	19253	2757	3042	3715	1769	2944	4106
;	super_101    	8	2	2	0	1	1	1	0	1
;	super_1023   	8	2	2	0	1	1	1	0	1
;	super_1058   	8	2	2	0	1	1	1	0	1
;	super_1068   	7	1	1	1	1	1	0	1	1
;	super_1097   	6	0	2	0	2	0	0	0	2
;	super_112    	31	10	10	2	2	2	1	2	2
;	super_1137   	3	0	1	0	1	0	0	0	1
;	super_1165   	14	3	3	0	2	2	2	0	2
;	super_1169   	45	0	15	0	15	0	0	0	15
;	super_120    	66	22	22	2	4	4	4	3	5
;	super_1257   	17	6	6	1	1	1	0	1	1
;	super_1265   	7	1	1	1	1	1	0	1	1
;	super_1287   	4	1	1	0	1	0	0	0	1
;	super_1318   	6	0	2	0	2	0	0	0	2
;	super_1334   	8	2	2	0	1	1	1	0	1
;	super_139    	38	13	13	0	3	3	3	0	3
;	super_1432   	6	1	1	0	1	1	1	0	1
;	super_1445   	6	1	1	0	1	1	1	0	1
;	super_1457   	6	0	2	0	2	0	0	0	2
;	super_154    	12	4	4	0	1	1	0	1	1
;	super_16     	172	1	56	1	56	1	0	1	56
;	super_164    	9	2	2	1	1	1	0	1	1
;	super_1650   	8	2	2	0	1	1	1	0	1
;	super_1713   	11	4	4	0	1	0	1	0	1
;	super_1717   	10	3	3	0	1	1	1	0	1
;	super_1741   	7	1	1	1	1	1	0	1	1
;	super_176    	33	9	9	3	2	3	1	3	3
;	super_1805   	30	0	10	0	10	0	0	0	10
;	super_1828   	6	1	1	0	1	1	1	0	1
;	super_199    	14	3	3	1	2	2	0	1	2
;	super_20     	16	4	4	1	2	1	1	1	2
;	super_2002   	9	2	2	1	1	1	0	1	1
;	super_2035   	19	5	5	2	1	2	0	2	2
;	super_2071   	8	2	2	0	1	1	1	0	1
;	super_2072   	3	0	1	0	1	0	0	0	1
;	super_2089   	6	0	2	0	2	0	0	0	2
;	super_2174   	5	1	1	0	1	1	0	0	1
;	super_2229   	17	3	4	1	2	3	0	0	4
;	super_2250   	8	2	2	0	1	1	1	0	1
;	super_2272   	3	0	1	0	1	0	0	0	1
;	super_2273   	6	1	1	0	1	1	1	0	1
;	super_2276   	12	4	4	0	1	1	1	0	1
;	super_229    	6	1	1	0	1	1	1	0	1
;	super_2410   	7	1	1	1	1	1	0	1	1
;	super_2414   	3	0	1	0	1	0	0	0	1
;	super_2454   	6	1	1	0	1	1	1	0	1
;	super_2493   	3	0	1	0	1	0	0	0	1
;	super_2518   	3	0	1	0	1	0	0	0	1
;	super_2540   	6	1	1	0	1	1	1	0	1
;	super_2553   	3	0	1	0	1	0	0	0	1
;	super_2600   	14	4	4	1	1	1	1	1	1
;	super_2635   	5	1	1	0	1	1	0	0	1
;	super_267    	10	3	3	0	1	1	1	0	1
;	super_2674   	17	4	4	2	1	2	0	2	2
;	super_2707   	3	0	1	0	1	0	0	0	1
;	super_2779   	10	2	2	1	1	1	1	1	1
;	super_2843   	6	1	1	0	1	1	1	0	1
;	super_2853   	7	2	2	0	1	0	1	0	1
;	super_2910   	28	7	7	2	1	3	3	2	3
;	super_2942   	7	1	1	1	1	1	0	1	1
;	super_296    	3	0	1	0	1	0	0	0	1
;	super_2967   	7	2	2	0	1	0	0	1	1
;	super_2969   	3	0	1	0	1	0	0	0	1
;	super_297    	6	1	1	0	1	1	1	0	1
;	super_2983   	7	1	1	1	1	1	0	1	1
;	super_3030   	3	0	1	0	1	0	0	0	1
;	super_3040   	8	3	3	0	1	0	0	0	1
;	super_3056   	8	1	1	1	1	1	1	1	1
;	super_3063   	27	0	9	0	9	0	0	0	9
;	super_31     	8	1	1	1	1	1	1	1	1
;	super_3113   	11	3	3	1	1	1	0	1	1
;	super_3132   	6	0	2	0	2	0	0	0	2
;	super_314    	8	2	2	0	1	1	1	0	1
;	super_3140   	6	0	2	0	2	0	0	0	2
;	super_3219   	5	1	1	0	1	1	0	0	1
;	super_3247   	10	3	3	0	1	1	1	0	1
;	super_3268   	6	2	2	0	1	0	0	0	1
;	super_3270   	9	2	2	1	1	1	0	1	1
;	super_3299   	12	2	2	1	1	2	1	1	2
;	super_35     	3	0	1	0	1	0	0	0	1
;	super_368    	10	3	3	0	1	1	1	0	1
;	super_400    	17	4	4	1	2	2	2	0	2
;	super_41     	7	1	1	1	1	1	1	0	1
;	super_444    	17	4	4	2	1	2	0	2	2
;	super_466    	82	30	31	3	1	5	4	3	5
;	super_49     	9	2	2	1	1	1	0	1	1
;	super_525    	9	3	3	0	1	1	0	0	1
;	super_527    	13	1	3	1	3	1	0	1	3
;	super_541    	14	5	5	0	1	1	1	0	1
;	super_57     	105	0	35	0	35	0	0	0	35
;	super_640    	9	2	2	1	1	1	1	0	1
;	super_70     	51	0	17	0	17	0	0	0	17
;	super_73     	67	28	28	2	2	2	1	2	2
;	super_814    	8	2	2	0	1	1	1	0	1
;	super_826    	5	1	1	0	1	0	1	0	1
;	super_836    	6	1	1	0	1	1	1	0	1
;	super_862    	9	2	2	1	1	1	0	1	1
;	super_88     	30	10	10	1	2	2	2	1	2
;	super_896    	11	4	4	0	1	0	1	0	1
;	super_99     	22	6	6	2	2	2	0	2	2
; Host name	baobab.eead.csic.es
; Job started	2018-09-25.054803
; Job done	2018-09-25.131921
; Seconds	104.44
;	user	104.44
;	system	39.29
;	cuser	24773.57
;	csystem	1680.55