; parse-gtf  -v 2 -i $RSAT/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40.gtf -fasta $RSAT/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40.pep.all.fa -org_name Oryza_glumaepatula.ALNU02000000.40 -task all -taxid 40148 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Oryza_glumaepatula.ALNU02000000.40/genome/Oryza_glumaepatula.ALNU02000000.40_exon.gtf
; Parsed rows per feature type
;	cds          	261620
;	exon         	280412
;	five_prime_utr	23082
;	gene         	39702
;	start_codon  	46831
;	stop_codon   	46757
;	three_prime_utr	24425
;	transcript   	50860
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	111098	37976	40539	3207	5441	6636	6627	3568	7104
;	10           	41665	14040	15004	1204	2235	2574	2563	1210	2835
;	11           	44179	14594	15572	1227	2616	2878	2867	1211	3214
;	12           	46695	15508	16756	1426	2471	2893	2890	1561	3190
;	2            	89706	30671	33010	2851	4348	5183	5179	2861	5603
;	3            	91538	31187	33369	2746	4567	5420	5414	2971	5864
;	4            	69180	23725	25299	1991	3392	4106	4097	2115	4455
;	5            	62692	21229	22735	1896	3236	3778	3767	1969	4082
;	6            	62788	21270	22671	1788	3242	3868	3871	1901	4177
;	7            	55913	18536	20052	1851	3001	3460	3452	1802	3759
;	8            	54095	18088	19512	1655	2827	3298	3297	1808	3610
;	9            	44140	14796	15893	1240	2326	2737	2733	1448	2967
; Host name	baobab.eead.csic.es
; Job started	2018-09-21.184815
; Job done	2018-09-21.231120
; Seconds	87.97
;	user	87.98
;	system	4.62
;	cuser	15504.07
;	csystem	237.76