; parse-gtf  -v 2 -i $RSAT/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40.gtf -fasta $RSAT/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40.pep.all.fa -org_name Oryza_punctata.AVCL00000000.40 -task all -taxid 4537 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Oryza_punctata.AVCL00000000.40/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Oryza_punctata.AVCL00000000.40/genome/Oryza_punctata.AVCL00000000.40_exon.gtf
; Parsed rows per feature type
;	cds          	246943
;	exon         	263484
;	five_prime_utr	19078
;	gene         	37791
;	start_codon  	41017
;	stop_codon   	41018
;	three_prime_utr	20594
;	transcript   	47089
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	101970	35697	37786	2606	5077	5758	5755	2859	6432
;	10           	37074	12452	13338	909	2161	2254	2256	1066	2638
;	11           	41837	13806	15075	1092	2526	2505	2505	1272	3056
;	12           	40093	13523	14626	1063	2220	2341	2343	1241	2736
;	2            	83155	29047	30923	2319	4190	4565	4566	2316	5229
;	3            	91836	32192	34131	2521	4469	5084	5086	2633	5720
;	4            	64209	22173	23661	1644	3366	3653	3648	1851	4213
;	5            	57272	19830	21078	1562	2990	3256	3254	1588	3714
;	6            	57227	19905	21066	1453	3007	3269	3272	1502	3753
;	7            	55107	18967	20143	1463	2933	3214	3214	1552	3621
;	8            	47891	16049	17432	1368	2663	2769	2766	1574	3270
;	9            	39343	13302	14225	1078	2189	2349	2353	1140	2707
; Host name	baobab.eead.csic.es
; Job started	2018-09-22.181559
; Job done	2018-09-22.231824
; Seconds	75.56
;	user	75.56
;	system	23.95
;	cuser	17222.63
;	csystem	585.92