; parse-gtf  -v 2 -i $RSAT/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI.gtf -fasta $RSAT/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI.pep.all.fa -org_name Brachypodium_hybridum.463.v1.1.JGI -task all -taxid 1071398 -gtf_source JGI -o $RSAT/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Brachypodium_hybridum.463.v1.1.JGI/genome/Brachypodium_hybridum.463.v1.1.JGI_exon.gtf
; Parsed rows per feature type
;	             	3
;	cds          	391741
;	five_prime_utr	68952
;	gene         	70160
;	mrna         	80980
;	three_prime_utr	66850
; Parsed rows per contig
;	Contig       	Total		cds	five_prime_utr	gene	mrna	three_prime_utr
;	##annot-version v1.1	1	1	0	0	0	0	0
;	##gff-version 3	1	1	0	0	0	0	0
;	##species Brachypodium hybridum	1	1	0	0	0	0	0
;	BhD1         	101108	0	58288	10065	10700	12241	9814
;	BhD2         	80399	0	46713	7865	8416	9671	7734
;	BhD3         	79215	0	45614	7890	8359	9590	7762
;	BhD4         	56830	0	31962	5528	6530	7370	5440
;	BhD5         	33470	0	18936	3303	3706	4215	3310
;	BhS1         	48322	0	28542	5085	4498	5376	4821
;	BhS10        	21063	0	12058	2182	2210	2565	2048
;	BhS2         	43192	0	25068	4599	4253	4939	4333
;	BhS3         	34748	0	20196	3613	3405	3999	3535
;	BhS4         	39053	0	22924	4118	3687	4326	3998
;	BhS5         	31169	0	17755	3260	3309	3780	3065
;	BhS6         	26055	0	14935	2649	2700	3129	2642
;	BhS7         	27481	0	16153	2785	2729	3176	2638
;	BhS8         	26545	0	15156	2853	2722	3137	2677
;	BhS9         	30033	0	17441	3157	2936	3466	3033
; Host name	baobab.eead.csic.es
; Job started	2021-03-04.075520
; Job done	2021-03-04.151120
; Seconds	76.8
;	user	76.8
;	system	12.83
;	cuser	25856.44
;	csystem	291.68