; parse-gtf  -v 2 -i $RSAT/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62.gtf -fasta $RSAT/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62.pep.all.fa -org_name Komagataella_phaffii_GS115.ASM174695v1.62 -task all -taxid 644223 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62.dna_rm.genome.fa
;	fasta        	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62.pep.all.fa
;	gtf          	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62.gtf
; Output files
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62_gene_end.gtf
;	tss_gtf      	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62_tss.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/contig_rm.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/start_codon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/organism.tab
;	transcript_gtf	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62_transcript.gtf
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/peptidic_sequences.fasta
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62_stop_codon.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/log.txt
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62_five_prime_utr.gtf
;	tts_gtf      	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62_tts.gtf
;	contig       	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/contig.tab
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/contigs_rm.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62.pep.all_lengths.tab
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/stop_codon.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62_three_prime_utr.gtf
;	gene         	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/gene.tab
;	cds          	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/cds.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62_start_codon.gtf
;	exon         	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/exon.tab
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/transcript.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62_exon.gtf
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62_gene_start.gtf
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/contigs.txt
;	gene_gtf     	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62_gene.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62.dna.toplevel_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Komagataella_phaffii_GS115.ASM174695v1.62/genome/Komagataella_phaffii_GS115.ASM174695v1.62.dna_rm.genome_lengths.tab
; Parsed rows per feature type
;	             	5223
;	cds          	5259
;	chromosome   	4
;	exon         	5426
;	five_prime_utr	2028
;	gene         	5035
;	mrna         	5064
;	ncrna_gene   	167
;	rrna         	44
;	supercontig  	6
;	three_prime_utr	2124
;	trna         	123
; Parsed rows per contig
;	Contig       	Total		cds	chromosome	exon	five_prime_utr	gene	mrna	ncrna_gene	rrna	supercontig	three_prime_utr	trna
;	###          	5212	5212	0	0	0	0	0	0	0	0	0	0	0
;	##gff-version 3	1	1	0	0	0	0	0	0	0	0	0	0	0
;	##sequence-region   1 1 2887587	1	1	0	0	0	0	0	0	0	0	0	0	0
;	##sequence-region   2 1 2396528	1	1	0	0	0	0	0	0	0	0	0	0	0
;	##sequence-region   3 1 2249375	1	1	0	0	0	0	0	0	0	0	0	0	0
;	##sequence-region   4 1 1831004	1	1	0	0	0	0	0	0	0	0	0	0	0
;	##sequence-region   CP014719.1 1 13861	1	1	0	0	0	0	0	0	0	0	0	0	0
;	##sequence-region   CP014720.1 1 31580	1	1	0	0	0	0	0	0	0	0	0	0	0
;	##sequence-region   CP014721.1 1 13305	1	1	0	0	0	0	0	0	0	0	0	0	0
;	##sequence-region   CP014722.1 1 14703	1	1	0	0	0	0	0	0	0	0	0	0	0
;	##sequence-region   CP014723.1 1 13388	1	1	0	0	0	0	0	0	0	0	0	0	0
;	##sequence-region   CP014724.1 1 11426	1	1	0	0	0	0	0	0	0	0	0	0	0
;	1            	7792	0	1614	1	1675	634	1539	1549	61	8	0	658	53
;	2            	6335	0	1318	1	1339	526	1275	1278	21	4	0	556	17
;	3            	6048	0	1271	1	1304	468	1218	1226	33	3	0	494	30
;	4            	5016	0	1051	1	1082	400	998	1006	31	8	0	416	23
;	CP014719.1   	13	0	0	0	4	0	0	0	4	4	1	0	0
;	CP014720.1   	25	0	0	0	8	0	0	0	8	8	1	0	0
;	CP014721.1   	4	0	0	0	1	0	0	0	1	1	1	0	0
;	CP014722.1   	13	0	0	0	4	0	0	0	4	4	1	0	0
;	CP014723.1   	13	0	0	0	4	0	0	0	4	4	1	0	0
;	CP014724.1   	21	0	5	0	5	0	5	5	0	0	1	0	0
; Host name	baobab
; Job started	2026-01-06.204207
; Job done	2026-01-06.204801
; Seconds	1.83
;	user	1.83
;	system	0.14
;	cuser	389.83
;	csystem	41.34