; parse-gtf  -v 2 -i $RSAT/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29.gtf -fasta $RSAT/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29.dna.genome.fa -fasta_rm $RSAT/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29.pep.all.fa -org_name Arabidopsis_thaliana.TAIR10.29 -task all -taxid 3702 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29.dna.genome.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29.dna.genome_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.29/genome/Arabidopsis_thaliana.TAIR10.29_exon.gtf
; Parsed rows per feature type
;	cds          	197130
;	exon         	217183
;	five_prime_utr	34621
;	gene         	33602
;	start_codon  	35411
;	stop_codon   	35394
;	three_prime_utr	30634
;	transcript   	41671
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	166981	53564	58387	9243	8433	9273	9266	8169	10646
;	2            	97423	29922	33516	5592	5513	5567	5563	4895	6855
;	3            	120882	37575	41822	6794	6730	6914	6912	5916	8219
;	4            	95725	30219	33392	5189	5140	5360	5359	4682	6384
;	5            	143106	45606	49745	7799	7507	8097	8092	6972	9288
;	Mt           	829	140	164	4	146	114	115	0	146
;	Pt           	700	104	157	0	133	86	87	0	133
; Host name	baobab.eead.csic.es
; Job started	2015-11-14.165736
; Job done	2015-11-14.185709
; Seconds	52.75
;	user	52.75
;	system	1.32
;	cuser	7075.7
;	csystem	77.34