; parse-gtf  -v 2 -i $RSAT/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI.gtf -fasta $RSAT/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI.pep.all.fa -org_name Phaseolus_vulgaris.442.v2.JGI -task all -taxid 3885 -gtf_source JGI -o $RSAT/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome
; Program version       	1.48
; Input files
;	gtf          	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI.dna.toplevel.fa
;	fasta_rm     	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI.dna_rm.genome.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI.pep.all.fa
; Output files
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/contig_rm.tab
;	exon         	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/exon.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/start_codon.tab
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/stop_codon.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI.dna_rm.genome_lengths.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI_tss.gtf
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI.pep.all_lengths.tab
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI_gene_end.gtf
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI_three_prime_utr.gtf
;	gene         	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/gene.tab
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/contigs_rm.txt
;	transcript_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI_transcript.gtf
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/contigs.txt
;	exon_gtf     	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI_exon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI_five_prime_utr.gtf
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/peptidic_sequences.fasta
;	organism     	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/organism.tab
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/transcript.tab
;	fasta_lengths	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI.dna.toplevel_lengths.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI_start_codon.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI_gene.gtf
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI_gene_start.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/log.txt
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI_stop_codon.gtf
;	contig       	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/contig.tab
;	cds          	/var/www/html/rsat/public_html/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/cds.tab
;	tts_gtf      	/var/www/html/rsat/data/genomes/Phaseolus_vulgaris.442.v2.JGI/genome/Phaseolus_vulgaris.442.v2.JGI_tts.gtf
; Parsed rows per feature type
;	             	3
;	cds          	218847
;	five_prime_utr	42711
;	gene         	27433
;	mrna         	36995
;	three_prime_utr	37094
; Parsed rows per contig
;	Contig       	Total		cds	five_prime_utr	gene	mrna	three_prime_utr
;	##annot-version v2.1	1	1	0	0	0	0	0
;	##gff-version 3	1	1	0	0	0	0	0
;	##species Phaseolus vulgaris	1	1	0	0	0	0	0
;	Chr01        	35582	0	21426	4253	2678	3601	3624
;	Chr02        	44809	0	26971	5418	3338	4539	4543
;	Chr03        	40692	0	24641	4744	3023	4094	4190
;	Chr04        	21099	0	12148	2481	1829	2345	2296
;	Chr05        	24167	0	14651	2861	1759	2415	2481
;	Chr06        	28540	0	17014	3401	2240	2962	2923
;	Chr07        	37325	0	22768	4402	2672	3695	3788
;	Chr08        	38400	0	23092	4495	2950	3980	3883
;	Chr09        	37167	0	22843	4277	2692	3631	3724
;	Chr10        	21818	0	13188	2532	1672	2270	2156
;	Chr11        	27494	0	16471	3169	2159	2866	2829
;	scaffold_100 	26	0	18	1	3	3	1
;	scaffold_104 	28	0	10	0	9	9	0
;	scaffold_1075	10	0	8	0	1	1	0
;	scaffold_1077	53	0	28	9	1	5	10
;	scaffold_1082	11	0	2	2	1	2	4
;	scaffold_109 	3	0	1	0	1	1	0
;	scaffold_1090	7	0	3	1	1	1	1
;	scaffold_1092	7	0	3	1	1	1	1
;	scaffold_1096	5	0	2	1	1	1	0
;	scaffold_1097	3	0	1	0	1	1	0
;	scaffold_1103	6	0	2	1	1	1	1
;	scaffold_1110	11	0	7	1	1	1	1
;	scaffold_1114	12	0	5	2	1	2	2
;	scaffold_1119	10	0	6	1	1	1	1
;	scaffold_112 	3	0	1	0	1	1	0
;	scaffold_1123	3	0	1	0	1	1	0
;	scaffold_1125	5	0	1	1	1	1	1
;	scaffold_1131	6	0	1	2	1	1	1
;	scaffold_1137	3	0	1	0	1	1	0
;	scaffold_1140	5	0	1	1	1	1	1
;	scaffold_1142	13	0	9	1	1	1	1
;	scaffold_1151	6	0	1	1	1	1	2
;	scaffold_1158	5	0	1	1	1	1	1
;	scaffold_1160	6	0	2	1	1	1	1
;	scaffold_1161	10	0	6	1	1	1	1
;	scaffold_1170	8	0	4	1	1	1	1
;	scaffold_1171	6	0	1	2	1	1	1
;	scaffold_1180	6	0	2	1	1	1	1
;	scaffold_1183	7	0	4	1	1	1	0
;	scaffold_1186	5	0	1	1	1	1	1
;	scaffold_1197	6	0	1	1	1	1	2
;	scaffold_12  	165	0	109	17	11	14	14
;	scaffold_1205	7	0	3	1	1	1	1
;	scaffold_1219	5	0	1	1	1	1	1
;	scaffold_1223	5	0	1	1	1	1	1
;	scaffold_128 	13	0	5	4	1	1	2
;	scaffold_13  	515	0	321	70	29	48	47
;	scaffold_132 	15	0	11	0	2	2	0
;	scaffold_133 	24	0	18	1	2	2	1
;	scaffold_138 	36	0	14	7	5	5	5
;	scaffold_14  	430	0	252	56	26	44	52
;	scaffold_142 	42	0	20	6	5	6	5
;	scaffold_146 	5	0	1	1	1	1	1
;	scaffold_15  	1450	0	820	180	102	150	198
;	scaffold_16  	85	0	38	13	10	12	12
;	scaffold_162 	17	0	5	3	3	3	3
;	scaffold_17  	371	0	214	44	26	40	47
;	scaffold_18  	33	0	13	5	5	6	4
;	scaffold_19  	34	0	16	4	1	4	9
;	scaffold_194 	5	0	1	1	1	1	1
;	scaffold_20  	29	0	15	3	4	4	3
;	scaffold_23  	180	0	142	13	6	10	9
;	scaffold_235 	156	0	119	14	3	8	12
;	scaffold_24  	5	0	1	1	1	1	1
;	scaffold_240 	37	0	24	3	4	4	2
;	scaffold_26  	21	0	14	2	2	2	1
;	scaffold_260 	6	0	4	0	1	1	0
;	scaffold_264 	22	0	14	2	1	2	3
;	scaffold_27  	8	0	3	1	2	2	0
;	scaffold_28  	70	0	38	7	9	9	7
;	scaffold_29  	87	0	50	15	5	8	9
;	scaffold_293 	13	0	9	0	2	2	0
;	scaffold_30  	710	0	483	77	26	52	72
;	scaffold_321 	5	0	1	1	1	1	1
;	scaffold_33  	31	0	19	2	4	4	2
;	scaffold_35  	17	0	7	2	3	3	2
;	scaffold_357 	4	0	2	0	1	1	0
;	scaffold_365 	14	0	10	0	2	2	0
;	scaffold_375 	4	0	2	0	1	1	0
;	scaffold_40  	9	0	7	0	1	1	0
;	scaffold_41  	232	0	200	10	2	10	10
;	scaffold_425 	18	0	6	2	2	2	6
;	scaffold_43  	32	0	21	3	3	3	2
;	scaffold_439 	9	0	7	0	1	1	0
;	scaffold_44  	56	0	33	5	6	6	6
;	scaffold_45  	6	0	4	0	1	1	0
;	scaffold_456 	6	0	2	1	1	1	1
;	scaffold_458 	11	0	2	2	1	2	4
;	scaffold_46  	7	0	2	2	1	1	1
;	scaffold_477 	24	0	18	1	2	2	1
;	scaffold_48  	6	0	2	1	1	1	1
;	scaffold_526 	10	0	2	1	1	1	5
;	scaffold_567 	8	0	4	1	1	1	1
;	scaffold_59  	70	0	44	7	7	7	5
;	scaffold_590 	20	0	16	0	2	2	0
;	scaffold_598 	9	0	5	1	1	1	1
;	scaffold_62  	4	0	2	0	1	1	0
;	scaffold_66  	186	0	159	7	4	8	8
;	scaffold_721 	7	0	3	1	1	1	1
;	scaffold_73  	76	0	47	6	8	9	6
;	scaffold_77  	18	0	6	6	2	2	2
;	scaffold_770 	5	0	1	1	1	1	1
;	scaffold_78  	19	0	11	2	2	2	2
;	scaffold_802 	3	0	1	0	1	1	0
;	scaffold_84  	48	0	11	10	10	10	7
;	scaffold_922 	48	0	28	5	1	5	9
;	scaffold_93  	6	0	2	1	1	1	1
;	scaffold_96  	14	0	10	1	1	1	1
;	scaffold_975 	49	0	24	7	2	6	10
; Host name	baobab
; Job started	2024-05-24.094950
; Job done	2024-05-24.145942
; Seconds	35.94
;	user	35.94
;	system	4.89
;	cuser	18323.85
;	csystem	261.76