; parse-gtf  -v 2 -i $RSAT/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR.gtf -fasta $RSAT/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR.pep.all.fa -org_name Prunus_avium.Satonishiki.PAV_r1.0.GDR -task all -taxid 42229 -gtf_source GDR -o $RSAT/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Prunus_avium.Satonishiki.PAV_r1.0.GDR/genome/Prunus_avium.Satonishiki.PAV_r1.0.GDR_exon.gtf
; Parsed rows per feature type
;	             	1
;	cds          	158448
;	exon         	168376
;	gene         	43673
; Parsed rows per contig
;	Contig       	Total		cds	exon	gene
;	##gff-version 3	1	1	0	0	0
;	PAV_r1.0chr0 	71514	0	29200	30093	12221
;	PAV_r1.0chr1 	66375	0	28784	30854	6737
;	PAV_r1.0chr2 	36442	0	15668	16825	3949
;	PAV_r1.0chr3 	33871	0	14664	15619	3588
;	PAV_r1.0chr4 	36581	0	15702	16753	4126
;	PAV_r1.0chr5 	27642	0	12015	12805	2822
;	PAV_r1.0chr6 	37178	0	16092	17248	3838
;	PAV_r1.0chr7 	31164	0	13510	14474	3180
;	PAV_r1.0chr8 	29730	0	12813	13705	3212
; Host name	baobab.eead.csic.es
; Job started	2017-12-15.122009
; Job done	2017-12-15.162302
; Seconds	31.55
;	user	31.56
;	system	9.39
;	cuser	14278.84
;	csystem	249.41