; parse-gtf  -v 2 -i $RSAT/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40.gtf -fasta $RSAT/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40.pep.all.fa -org_name Arabidopsis_thaliana.TAIR10.40 -task all -taxid 3702 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Arabidopsis_thaliana.TAIR10.40/genome/Arabidopsis_thaliana.TAIR10.40_exon.gtf
; Parsed rows per feature type
;	cds          	285977
;	exon         	315381
;	five_prime_utr	56384
;	gene         	34262
;	start_codon  	48315
;	stop_codon   	48313
;	three_prime_utr	48308
;	transcript   	55442
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	239305	77497	85413	14888	8933	12645	12645	12711	14573
;	2            	138015	43789	48473	8981	5305	7596	7592	7588	8691
;	3            	173108	54839	60762	11100	6975	9468	9467	9429	11068
;	4            	136924	44043	48457	8572	5067	7423	7417	7565	8380
;	5            	203377	65570	71911	12839	7660	10984	10990	11015	12408
;	Mt           	878	135	183	4	164	113	115	0	164
;	Pt           	775	104	182	0	158	86	87	0	158
; Host name	baobab.eead.csic.es
; Job started	2018-09-12.214515
; Job done	2018-09-13.000907
; Seconds	72.9
;	user	72.9
;	system	3.55
;	cuser	8492.5
;	csystem	106.04