; parse-gtf  -v 2 -i $RSAT/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40.gtf -fasta $RSAT/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40.pep.all.fa -org_name Oryza_barthii.O.barthii_v1.40 -task all -taxid 65489 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Oryza_barthii.O.barthii_v1.40/genome/Oryza_barthii.O.barthii_v1.40_exon.gtf
; Parsed rows per feature type
;	cds          	231562
;	exon         	243647
;	five_prime_utr	17362
;	gene         	37849
;	start_codon  	41525
;	stop_codon   	41497
;	three_prime_utr	17933
;	transcript   	44891
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	93103	32404	33879	2397	4902	5559	5556	2489	5917
;	10           	36287	12151	12882	894	2143	2341	2339	1003	2534
;	11           	44184	14872	15659	1095	2575	2889	2881	1102	3111
;	12           	38214	12855	13606	1007	2205	2424	2424	1058	2635
;	2            	79322	27758	29117	2077	4196	4596	4591	2001	4986
;	3            	83362	28791	30257	2225	4561	4965	4963	2210	5390
;	4            	59835	20598	21671	1475	3358	3642	3641	1470	3980
;	5            	54404	18733	19633	1328	3060	3341	3347	1343	3619
;	6            	52456	17893	18759	1239	3056	3304	3298	1340	3567
;	7            	51325	17403	18282	1372	2962	3224	3219	1388	3475
;	8            	45222	15087	16182	1234	2613	2793	2796	1477	3040
;	9            	38552	13017	13720	1019	2218	2447	2442	1052	2637
; Host name	baobab.eead.csic.es
; Job started	2018-09-21.052522
; Job done	2018-09-21.093822
; Seconds	75.21
;	user	75.21
;	system	2.39
;	cuser	14989.85
;	csystem	161.73