; parse-gtf  -v 2 -i $RSAT/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57.gtf -fasta $RSAT/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57.pep.all.fa -org_name Secale_cereale.Rye_Lo7_2018_v1p1p1.57 -task all -taxid 4550 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome
; Program version       	1.48
; Input files
;	gtf          	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57.gtf
;	fasta_rm     	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57.dna_rm.genome.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57.pep.all.fa
;	fasta        	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57.dna.toplevel.fa
; Output files
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57.dna_rm.genome_lengths.tab
;	cds          	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/cds.tab
;	tts_gtf      	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57_tts.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/log.txt
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/start_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57_start_codon.gtf
;	exon         	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/exon.tab
;	transcript_gtf	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57_transcript.gtf
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/contigs.txt
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/stop_codon.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/contig.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/gene.tab
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/peptidic_sequences.fasta
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57_gene_start.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57_gene.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/transcript.tab
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/contig_rm.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57_three_prime_utr.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57_gene_end.gtf
;	exon_gtf     	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57_exon.gtf
;	tss_gtf      	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57_tss.gtf
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57.pep.all_lengths.tab
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57_five_prime_utr.gtf
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57_stop_codon.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/Secale_cereale.Rye_Lo7_2018_v1p1p1.57.dna.toplevel_lengths.tab
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/contigs_rm.txt
;	organism     	/var/www/html/rsat/public_html/data/genomes/Secale_cereale.Rye_Lo7_2018_v1p1p1.57/genome/organism.tab
; Parsed rows per feature type
;	cds          	152217
;	exon         	152231
;	five_prime_utr	2
;	gene         	34441
;	start_codon  	34441
;	stop_codon   	34441
;	transcript   	34441
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	transcript
;	0R           	20688	6465	6467	0	1939	1939	1939	1939
;	1R           	53820	18820	18820	0	4045	4045	4045	4045
;	2R           	65824	22813	22815	0	5049	5049	5049	5049
;	3R           	59041	20700	20701	0	4410	4410	4410	4410
;	4R           	61082	20865	20867	2	4837	4837	4837	4837
;	5R           	66542	22959	22963	0	5155	5155	5155	5155
;	6R           	56851	19510	19513	0	4457	4457	4457	4457
;	7R           	58366	20085	20085	0	4549	4549	4549	4549
; Host name	baobab
; Job started	2023-12-04.120528
; Job done	2023-12-06.140503
; Seconds	358.71
;	user	358.71
;	system	58.27
;	cuser	176556.82
;	csystem	2788.48