; parse-gtf  -v 2 -i $RSAT/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI.gtf -fasta $RSAT/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI.pep.all.fa -org_name Solanum_lycopersicum.ITAG4.0.JGI -task all -taxid 4081 -gtf_source JGI -o $RSAT/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI.pep.all.fa
; Output files
;	fasta_lengths	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI.dna.toplevel_lengths.tab
;	transcript_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI_transcript.gtf
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI_stop_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI_five_prime_utr.gtf
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI.dna_rm.genome_lengths.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI_start_codon.gtf
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/peptidic_sequences.fasta
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/start_codon.tab
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI.pep.all_lengths.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI_tss.gtf
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/log.txt
;	gene_gtf     	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI_gene.gtf
;	tts_gtf      	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI_tts.gtf
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/contigs.txt
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI_gene_end.gtf
;	contig       	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/contig.tab
;	cds          	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/cds.tab
;	exon         	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/exon.tab
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/contigs_rm.txt
;	exon_gtf     	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI_exon.gtf
;	organism     	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/organism.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/gene.tab
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/stop_codon.tab
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/transcript.tab
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/contig_rm.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Solanum_lycopersicum.ITAG4.0.JGI/genome/Solanum_lycopersicum.ITAG4.0.JGI_gene_start.gtf
; Parsed rows per feature type
;	             	6
;	cds          	153474
;	five_prime_utr	21452
;	gene         	34075
;	mrna         	34075
;	three_prime_utr	22835
; Parsed rows per contig
;	Contig       	Total		cds	five_prime_utr	gene	mrna	three_prime_utr
;	##annot-site ITAG	1	1	0	0	0	0	0
;	##annot-version ITAG4.0	1	1	0	0	0	0	0
;	##assembly-site SGN	1	1	0	0	0	0	0
;	##assembly-version SL4.0	1	1	0	0	0	0	0
;	##gff-version 3	1	1	0	0	0	0	0
;	##species Solanum lycopersicum	1	1	0	0	0	0	0
;	SL4.0ch00    	2376	0	1120	126	513	513	104
;	SL4.0ch01    	34265	0	19777	2950	4133	4133	3272
;	SL4.0ch02    	27047	0	15671	2216	3379	3379	2402
;	SL4.0ch03    	26639	0	15544	2171	3324	3324	2276
;	SL4.0ch04    	22172	0	12786	1807	2819	2819	1941
;	SL4.0ch05    	18017	0	9976	1562	2382	2382	1715
;	SL4.0ch06    	22460	0	13085	1855	2769	2769	1982
;	SL4.0ch07    	19618	0	11325	1515	2517	2517	1744
;	SL4.0ch08    	19264	0	11245	1502	2428	2428	1661
;	SL4.0ch09    	19391	0	11072	1578	2521	2521	1699
;	SL4.0ch10    	18251	0	10362	1459	2520	2520	1390
;	SL4.0ch11    	17856	0	10605	1307	2326	2326	1292
;	SL4.0ch12    	18555	0	10906	1404	2444	2444	1357
; Host name	baobab
; Job started	2023-11-13.132618
; Job done	2023-11-13.203910
; Seconds	50.83
;	user	50.83
;	system	8.91
;	cuser	25622.8
;	csystem	330.85