; parse-gtf  -v 2 -i $RSAT/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI.gtf -fasta $RSAT/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI.pep.all.fa -org_name Brachypodium_distachyon.556.v3.2.JGI -task all -taxid 15368 -gtf_source JGI -o $RSAT/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI.gtf
;	fasta_pep    	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI.pep.all.fa
;	fasta        	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI.dna.toplevel.fa
; Output files
;	contig       	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/contig.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/start_codon.tab
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/contig_rm.tab
;	gene_gtf     	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI_gene.gtf
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI.dna_rm.genome_lengths.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/gene.tab
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI.pep.all_lengths.tab
;	cds          	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/cds.tab
;	fasta_lengths	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI.dna.toplevel_lengths.tab
;	transcript_gtf	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI_transcript.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/transcript.tab
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI_gene_end.gtf
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI_five_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/log.txt
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/peptidic_sequences.fasta
;	exon         	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/exon.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI_stop_codon.gtf
;	tss_gtf      	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/stop_codon.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI_gene_start.gtf
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/contigs.txt
;	exon_gtf     	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI_exon.gtf
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI_three_prime_utr.gtf
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/contigs_rm.txt
;	organism     	/var/www/html/rsat/public_html/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/organism.tab
;	tts_gtf      	/var/www/html/rsat/data/genomes/Brachypodium_distachyon.556.v3.2.JGI/genome/Brachypodium_distachyon.556.v3.2.JGI_tts.gtf
; Parsed rows per feature type
;	             	3
;	cds          	363981
;	five_prime_utr	66236
;	gene         	32439
;	mrna         	56847
;	three_prime_utr	63053
; Parsed rows per contig
;	Contig       	Total		cds	five_prime_utr	gene	mrna	three_prime_utr
;	##annot-version v3.2	1	1	0	0	0	0	0
;	##gff-version 3	1	1	0	0	0	0	0
;	##species Brachypodium distachyon	1	1	0	0	0	0	0
;	Bd1          	177080	0	112393	19596	9415	16835	18841
;	Bd1_centromere_containing_Bradi1g41430	30	0	13	5	2	5	5
;	Bd2          	130019	0	81661	14589	7227	12584	13958
;	Bd3          	133180	0	83660	15198	7118	12792	14412
;	Bd4          	87652	0	52484	10532	5487	9183	9966
;	Bd5          	54556	0	33752	6312	3185	5441	5866
;	scaffold_12  	25	0	10	4	2	4	5
;	scaffold_135 	6	0	4	0	1	1	0
;	scaffold_14  	3	0	1	0	1	1	0
;	scaffold_180 	5	0	3	0	1	1	0
; Host name	baobab
; Job started	2023-06-12.095955
; Job done	2023-06-12.133212
; Seconds	32.59
;	user	32.59
;	system	2.64
;	cuser	12557.47
;	csystem	187.6