; parse-gtf  -v 2 -i $RSAT/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29.gtf -fasta $RSAT/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29.dna.genome.fa -fasta_rm $RSAT/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29.pep.all.fa -org_name Zea_mays.AGPv3.29 -task all -taxid 4577 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Zea_mays.AGPv3.29/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29.dna.genome.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29.dna.genome_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Zea_mays.AGPv3.29/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Zea_mays.AGPv3.29/genome/Zea_mays.AGPv3.29_exon.gtf
; Parsed rows per feature type
;	cds          	291534
;	exon         	330421
;	five_prime_utr	72706
;	gene         	39625
;	start_codon  	62155
;	stop_codon   	61276
;	three_prime_utr	69367
;	transcript   	63391
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	154689	45670	51724	11417	6022	9669	9541	10808	9838
;	10           	65571	19117	21767	4828	2706	4174	4093	4644	4242
;	2            	116513	34259	38813	8494	4765	7325	7253	8119	7485
;	3            	104818	31227	35202	7374	4189	6500	6417	7286	6623
;	4            	105568	30932	35071	7966	4201	6675	6602	7316	6805
;	5            	116092	34534	39048	8382	4495	7146	7056	8129	7302
;	6            	82199	24146	27400	6201	3287	5134	5080	5698	5253
;	7            	78476	22934	26119	5851	3124	4940	4854	5616	5038
;	8            	87780	25816	29142	6426	3518	5563	5483	6158	5674
;	9            	75666	22200	25374	5572	2998	4697	4648	5385	4792
;	Mt           	836	147	147	17	123	126	125	25	126
;	Pt           	357	57	58	18	51	52	52	17	52
;	scaffold_107 	9	1	2	2	1	1	0	1	1
;	scaffold_108 	7	1	1	1	1	1	0	1	1
;	scaffold_112 	8	1	2	2	1	1	0	0	1
;	scaffold_12  	7	1	1	1	1	1	0	1	1
;	scaffold_121 	11	2	3	2	1	1	0	1	1
;	scaffold_123 	8	2	2	0	1	1	0	1	1
;	scaffold_13  	7	1	1	1	1	1	0	1	1
;	scaffold_130 	15	1	5	5	1	1	0	1	1
;	scaffold_133 	11	3	3	1	1	1	0	1	1
;	scaffold_134 	26	7	8	2	1	2	1	3	2
;	scaffold_137 	23	6	7	2	1	2	1	2	2
;	scaffold_141 	7	1	1	1	1	1	0	1	1
;	scaffold_145 	14	4	4	1	1	1	1	1	1
;	scaffold_147 	14	5	5	1	1	1	0	0	1
;	scaffold_148 	8	2	2	1	1	1	0	0	1
;	scaffold_153 	12	4	4	1	1	0	0	1	1
;	scaffold_157 	14	3	4	1	1	1	1	2	1
;	scaffold_158 	6	1	1	1	1	0	0	1	1
;	scaffold_163 	9	2	2	1	1	1	0	1	1
;	scaffold_167 	5	1	1	0	1	0	0	1	1
;	scaffold_17  	14	4	4	1	1	1	1	1	1
;	scaffold_175 	6	1	1	1	1	0	0	1	1
;	scaffold_176 	12	2	3	1	1	1	1	2	1
;	scaffold_177 	7	1	1	1	1	1	0	1	1
;	scaffold_179 	9	1	2	1	1	1	0	2	1
;	scaffold_181 	12	2	3	2	1	1	1	1	1
;	scaffold_19  	7	1	1	1	1	1	0	1	1
;	scaffold_192 	7	1	1	1	1	1	0	1	1
;	scaffold_198 	11	3	3	1	1	1	0	1	1
;	scaffold_2   	9	2	2	1	1	1	0	1	1
;	scaffold_201 	9	2	2	1	1	1	0	1	1
;	scaffold_203 	64	25	27	4	1	2	1	2	2
;	scaffold_206 	8	2	2	1	1	1	0	0	1
;	scaffold_210 	29	11	12	2	1	1	0	1	1
;	scaffold_211 	9	1	2	1	1	1	0	2	1
;	scaffold_212 	12	3	3	1	1	1	1	1	1
;	scaffold_216 	7	1	1	1	1	1	0	1	1
;	scaffold_217 	7	1	1	1	1	1	0	1	1
;	scaffold_229 	23	8	9	2	1	1	0	1	1
;	scaffold_240 	7	1	1	1	1	1	0	1	1
;	scaffold_243 	7	1	1	1	1	1	0	1	1
;	scaffold_246 	9	2	2	1	1	1	0	1	1
;	scaffold_252 	7	1	1	1	1	1	0	1	1
;	scaffold_253 	14	4	4	1	1	1	1	1	1
;	scaffold_256 	9	2	2	1	1	1	0	1	1
;	scaffold_257 	9	2	2	1	1	1	0	1	1
;	scaffold_26  	22	8	8	1	1	1	1	1	1
;	scaffold_260 	18	5	6	2	1	1	1	1	1
;	scaffold_262 	9	1	2	1	1	1	0	2	1
;	scaffold_268 	6	1	1	1	1	1	0	0	1
;	scaffold_281 	20	7	7	1	1	1	1	1	1
;	scaffold_284 	12	3	3	1	1	1	1	1	1
;	scaffold_286 	11	2	3	2	1	1	0	1	1
;	scaffold_288 	14	1	4	4	1	1	1	1	1
;	scaffold_29  	6	1	1	1	1	0	0	1	1
;	scaffold_290 	7	1	1	1	1	1	0	1	1
;	scaffold_299 	24	8	9	2	1	1	1	1	1
;	scaffold_303 	9	2	2	1	1	1	0	1	1
;	scaffold_304 	7	1	1	1	1	1	0	1	1
;	scaffold_309 	9	1	2	2	1	1	0	1	1
;	scaffold_324 	7	1	1	1	1	1	0	1	1
;	scaffold_333 	19	7	7	1	1	1	1	0	1
;	scaffold_335 	11	3	3	1	1	1	0	1	1
;	scaffold_336 	7	1	1	1	1	1	0	1	1
;	scaffold_345 	16	6	6	1	1	1	0	0	1
;	scaffold_35  	7	1	1	1	1	1	0	1	1
;	scaffold_354 	7	1	1	1	1	1	0	1	1
;	scaffold_355 	7	1	1	1	1	1	0	1	1
;	scaffold_360 	18	7	7	1	1	1	0	0	1
;	scaffold_364 	16	3	5	1	1	1	1	3	1
;	scaffold_369 	7	1	1	1	1	1	0	1	1
;	scaffold_373 	9	2	2	1	1	1	0	1	1
;	scaffold_376 	16	3	5	1	1	1	1	3	1
;	scaffold_384 	7	1	1	1	1	1	0	1	1
;	scaffold_391 	13	3	4	2	1	1	0	1	1
;	scaffold_396 	7	1	1	1	1	1	0	1	1
;	scaffold_4   	7	1	1	1	1	1	0	1	1
;	scaffold_401 	7	1	1	1	1	1	0	1	1
;	scaffold_406 	15	3	3	2	1	2	0	2	2
;	scaffold_412 	44	11	15	4	1	3	1	6	3
;	scaffold_42  	7	1	1	1	1	1	0	1	1
;	scaffold_426 	9	2	2	1	1	1	0	1	1
;	scaffold_429 	7	1	1	1	1	1	0	1	1
;	scaffold_433 	16	5	5	1	1	1	1	1	1
;	scaffold_434 	9	2	2	1	1	1	0	1	1
;	scaffold_439 	9	1	2	1	1	1	0	2	1
;	scaffold_440 	20	6	7	2	1	1	1	1	1
;	scaffold_448 	9	1	2	1	1	1	0	2	1
;	scaffold_457 	6	1	1	1	1	1	0	0	1
;	scaffold_46  	7	1	1	1	1	1	0	1	1
;	scaffold_465 	12	2	3	1	1	1	1	2	1
;	scaffold_469 	18	5	6	2	1	1	1	1	1
;	scaffold_480 	9	2	2	1	1	1	0	1	1
;	scaffold_483 	9	1	2	2	1	1	0	1	1
;	scaffold_484 	11	2	3	1	1	1	0	2	1
;	scaffold_485 	8	2	2	1	1	1	0	0	1
;	scaffold_49  	9	2	2	1	1	1	0	1	1
;	scaffold_490 	5	1	1	0	1	0	0	1	1
;	scaffold_492 	7	1	1	1	1	1	0	1	1
;	scaffold_496 	14	2	2	1	2	2	2	1	2
;	scaffold_498 	15	2	2	2	2	2	2	1	2
;	scaffold_5   	12	3	3	1	1	1	1	1	1
;	scaffold_501 	256	99	112	0	3	8	8	18	8
;	scaffold_502 	58	18	18	1	5	5	5	1	5
;	scaffold_507 	109	30	30	5	9	10	10	5	10
;	scaffold_508 	102	22	26	8	9	9	10	8	10
;	scaffold_509 	23	4	4	1	3	3	3	2	3
;	scaffold_51  	7	1	1	1	1	1	0	1	1
;	scaffold_510 	16	5	5	1	1	1	1	1	1
;	scaffold_511 	16	5	5	1	1	1	1	1	1
;	scaffold_58  	32	8	9	3	1	3	1	4	3
;	scaffold_6   	12	3	3	1	1	1	1	1	1
;	scaffold_63  	11	2	3	1	1	1	0	2	1
;	scaffold_67  	7	1	1	1	1	1	0	1	1
;	scaffold_71  	7	1	1	1	1	1	0	1	1
;	scaffold_86  	7	1	1	1	1	1	0	1	1
;	scaffold_89  	12	3	3	1	1	1	1	1	1
;	scaffold_94  	14	4	4	1	1	1	1	1	1
;	scaffold_98  	14	4	4	1	1	1	1	1	1
;	scaffold_99  	13	4	4	1	1	1	0	1	1
; Host name	baobab.eead.csic.es
; Job started	2015-11-25.164416
; Job done	2015-11-26.114313
; Seconds	192.24
;	user	192.25
;	system	540.08
;	cuser	60268.64
;	csystem	6411.81