; parse-gtf  -v 2 -i $RSAT/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN.gtf -fasta $RSAT/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN.pep.all.fa -org_name Solanum_lycopersicum.SL5.0.SGN -task all -taxid 4081 -gtf_source SGN -o $RSAT/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome
; Program version       	1.48
; Input files
;	fasta        	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN.dna.toplevel.fa
;	gtf          	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN.gtf
;	fasta_pep    	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN.pep.all.fa
;	fasta_rm     	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN.dna_rm.genome.fa
; Output files
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/contigs.txt
;	gene         	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/gene.tab
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/contig_rm.tab
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN.pep.all_lengths.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN_stop_codon.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/stop_codon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/organism.tab
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/contigs_rm.txt
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN_three_prime_utr.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN.dna.toplevel_lengths.tab
;	exon         	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/exon.tab
;	transcript_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN_transcript.gtf
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN_five_prime_utr.gtf
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN_gene_start.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN_gene.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/log.txt
;	tss_gtf      	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN_tss.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN_gene_end.gtf
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/peptidic_sequences.fasta
;	exon_gtf     	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN_exon.gtf
;	tts_gtf      	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN_tts.gtf
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/Solanum_lycopersicum.SL5.0.SGN.dna_rm.genome_lengths.tab
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/transcript.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/contig.tab
;	cds          	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/genome/cds.tab
; Parsed rows per feature type
;	cds          	239549
;	exon         	257620
;	five_prime_utr	30023
;	gene         	36648
;	mrna         	43752
;	three_prime_utr	30046
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	mrna	three_prime_utr
;	0            	448	158	159	7	54	61	9
;	1            	81247	30846	33208	3587	4448	5325	3833
;	10           	45103	16559	17786	2231	2966	3444	2117
;	11           	45189	17261	18397	1920	2600	3079	1932
;	12           	45765	16871	18178	2184	2878	3366	2288
;	2            	61584	23254	25408	2987	3105	3826	3004
;	3            	65890	24773	26712	3193	3605	4368	3239
;	4            	52134	19562	21018	2400	3066	3654	2434
;	5            	45021	16730	17923	2186	2787	3286	2109
;	6            	50545	19200	20362	2507	2797	3326	2353
;	7            	49222	18590	19938	2190	2838	3423	2243
;	8            	47589	17832	19331	2402	2599	3159	2266
;	9            	47901	17913	19200	2229	2905	3435	2219
; Host name	baobab
; Job started	2023-04-26.093306
; Job done	2023-04-26.170009
; Seconds	58.81
;	user	58.81
;	system	7.26
;	cuser	26463.65
;	csystem	336.46