; parse-gtf  -v 2 -i $RSAT/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40.gtf -fasta $RSAT/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40.pep.all.fa -org_name Phaseolus_vulgaris.PhaVulg1_0.40 -task all -taxid 3885 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.PhaVulg1_0.40/genome/Phaseolus_vulgaris.PhaVulg1_0.40_exon.gtf
; Parsed rows per feature type
;	cds          	175879
;	exon         	176251
;	five_prime_utr	23608
;	gene         	28472
;	start_codon  	30995
;	stop_codon   	15545
;	three_prime_utr	23578
;	transcript   	33058
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	51164	17785	17816	2416	2806	3121	1509	2417	3294
;	10           	30277	10437	10464	1366	1747	1868	999	1369	2027
;	11           	39488	13636	13666	1789	2280	2448	1267	1768	2634
;	2            	63112	21913	21958	2967	3477	3843	1936	2968	4050
;	3            	56868	19902	19937	2617	3093	3410	1677	2634	3598
;	4            	30345	10200	10212	1430	1900	1968	1062	1410	2163
;	5            	35354	12343	12370	1596	1952	2132	1078	1602	2281
;	6            	40394	13880	13904	1936	2317	2509	1247	1927	2674
;	7            	53857	18821	18878	2497	2945	3218	1576	2510	3412
;	8            	52254	17814	17857	2493	3061	3311	1685	2491	3542
;	9            	52876	18765	18793	2430	2743	3055	1438	2428	3224
;	scaffold_103 	25	9	9	1	2	1	0	1	2
;	scaffold_107 	5	1	1	0	1	0	1	0	1
;	scaffold_109 	10	3	3	0	1	1	1	0	1
;	scaffold_118 	10	3	3	0	1	1	1	0	1
;	scaffold_119 	13	5	5	0	1	1	0	0	1
;	scaffold_12  	61	17	17	5	6	4	3	2	7
;	scaffold_122 	9	2	2	1	1	1	0	1	1
;	scaffold_135 	13	3	3	1	2	1	1	0	2
;	scaffold_139 	3	0	1	0	1	0	0	0	1
;	scaffold_14  	74	21	21	5	8	4	3	3	9
;	scaffold_16  	51	12	12	2	7	6	5	0	7
;	scaffold_161 	25	9	9	1	2	1	1	0	2
;	scaffold_164 	6	1	1	0	1	1	1	0	1
;	scaffold_166 	11	3	3	1	1	1	0	1	1
;	scaffold_169 	8	2	2	0	1	1	1	0	1
;	scaffold_17  	47	11	11	1	6	6	4	1	7
;	scaffold_173 	8	1	1	1	1	1	1	1	1
;	scaffold_175 	6	1	1	0	1	1	1	0	1
;	scaffold_183 	23	9	9	1	1	1	0	1	1
;	scaffold_191 	17	7	7	0	1	0	0	1	1
;	scaffold_193 	18	5	5	0	2	2	2	0	2
;	scaffold_196 	13	4	4	1	1	1	0	1	1
;	scaffold_198 	12	3	3	0	2	1	1	0	2
;	scaffold_199 	8	1	1	1	1	1	1	1	1
;	scaffold_204 	3	0	1	0	1	0	0	0	1
;	scaffold_206 	6	1	1	0	1	1	1	0	1
;	scaffold_22  	13	3	3	0	2	1	2	0	2
;	scaffold_225 	8	2	2	0	1	1	1	0	1
;	scaffold_227 	33	0	11	0	11	0	0	0	11
;	scaffold_231 	31	9	9	3	1	3	0	3	3
;	scaffold_233 	6	1	1	0	1	1	1	0	1
;	scaffold_237 	5	1	1	0	1	0	0	1	1
;	scaffold_24  	57	19	19	3	4	4	1	3	4
;	scaffold_243 	20	8	8	1	1	1	0	0	1
;	scaffold_25  	9	2	2	1	1	1	0	1	1
;	scaffold_255 	12	3	3	1	1	1	1	1	1
;	scaffold_265 	6	1	1	0	1	1	1	0	1
;	scaffold_273 	16	4	4	1	1	2	1	1	2
;	scaffold_281 	9	3	3	0	1	1	0	0	1
;	scaffold_287 	6	1	1	0	1	1	1	0	1
;	scaffold_29  	12	4	4	0	1	1	1	0	1
;	scaffold_299 	11	3	3	1	1	1	0	1	1
;	scaffold_31  	10	3	3	0	1	1	1	0	1
;	scaffold_32  	44	12	12	4	4	4	0	4	4
;	scaffold_332 	9	2	2	1	1	1	1	0	1
;	scaffold_36  	27	8	8	0	3	2	3	0	3
;	scaffold_368 	7	2	2	0	1	0	0	1	1
;	scaffold_369 	10	3	3	1	1	1	0	0	1
;	scaffold_38  	27	11	11	1	1	1	0	1	1
;	scaffold_382 	7	1	1	0	1	1	1	1	1
;	scaffold_395 	7	1	1	1	1	1	1	0	1
;	scaffold_399 	14	4	4	1	1	1	1	1	1
;	scaffold_40  	25	8	8	2	2	2	1	0	2
;	scaffold_416 	6	1	1	0	1	1	1	0	1
;	scaffold_42  	34	9	9	3	3	3	1	3	3
;	scaffold_43  	9	2	2	1	1	1	0	1	1
;	scaffold_432 	8	2	2	0	1	1	1	0	1
;	scaffold_46  	13	4	4	1	1	1	0	1	1
;	scaffold_47  	37	7	7	4	6	4	1	2	6
;	scaffold_48  	11	3	3	1	1	1	0	1	1
;	scaffold_51  	6	1	1	0	1	1	1	0	1
;	scaffold_53  	15	5	5	1	1	1	0	1	1
;	scaffold_57  	19	5	5	0	3	1	1	1	3
;	scaffold_59  	23	7	7	0	3	0	3	0	3
;	scaffold_596 	7	1	1	1	1	1	0	1	1
;	scaffold_61  	10	2	2	1	1	1	1	1	1
;	scaffold_62  	7	1	1	1	1	1	0	1	1
;	scaffold_65  	41	15	15	1	3	2	1	1	3
;	scaffold_658 	6	1	1	1	1	1	0	0	1
;	scaffold_66  	35	12	12	2	2	2	1	2	2
;	scaffold_67  	5	1	1	0	1	1	0	0	1
;	scaffold_68  	12	4	4	0	1	1	1	0	1
;	scaffold_69  	33	14	14	1	1	1	0	1	1
;	scaffold_71  	11	2	2	1	2	1	1	0	2
;	scaffold_731 	8	2	2	0	1	1	1	0	1
;	scaffold_74  	26	5	5	3	5	1	2	0	5
;	scaffold_740 	4	1	1	0	1	0	0	0	1
;	scaffold_752 	7	1	1	1	1	1	0	1	1
;	scaffold_793 	6	1	1	0	1	1	1	0	1
;	scaffold_883 	6	1	1	0	1	1	1	0	1
;	scaffold_91  	10	2	2	1	1	1	1	1	1
;	scaffold_92  	50	17	17	2	2	4	2	2	4
;	scaffold_93  	6	1	1	0	1	1	1	0	1
; Host name	baobab.eead.csic.es
; Job started	2018-09-23.110646
; Job done	2018-09-23.161832
; Seconds	77.77
;	user	77.77
;	system	21.56
;	cuser	18055.74
;	csystem	534.16