; parse-gtf  -v 2 -i $RSAT/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34.gtf -fasta $RSAT/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34.pep.all.fa -org_name Toxoplasma_gondii_fou.TGFOU1v02.34 -task all -taxid 943167 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome
; Program version       	1.48
; Input files
;	fasta        	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34.dna.toplevel.fa
;	fasta_rm     	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34.dna_rm.genome.fa
;	gtf          	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34.gtf
;	fasta_pep    	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34.pep.all.fa
; Output files
;	peptidic_sequences	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/peptidic_sequences.fasta
;	gene_end_gtf 	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34_gene_end.gtf
;	contig_rm    	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/contig_rm.tab
;	exon         	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/exon.tab
;	fasta_rm_lengths	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34.dna_rm.genome_lengths.tab
;	fasta_lengths	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34.dna.toplevel_lengths.tab
;	transcript   	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/transcript.tab
;	tts_gtf      	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34_tts.gtf
;	tss_gtf      	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34_tss.gtf
;	gene_start_gtf	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34_gene_start.gtf
;	gene_gtf     	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34_gene.gtf
;	three_prime_utr_gtf	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34_three_prime_utr.gtf
;	stop_codon_gtf	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34_stop_codon.gtf
;	gene         	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/gene.tab
;	log          	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/log.txt
;	contig       	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/contig.tab
;	fasta_pep_lengths	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34.pep.all_lengths.tab
;	start_codon  	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/start_codon.tab
;	contigs_txt  	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/contigs.txt
;	stop_codon   	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/stop_codon.tab
;	exon_gtf     	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34_exon.gtf
;	start_codon_gtf	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34_start_codon.gtf
;	contigs_txt_rm	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/contigs_rm.txt
;	transcript_gtf	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34_transcript.gtf
;	organism     	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/organism.tab
;	five_prime_utr_gtf	/export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/Toxoplasma_gondii_fou.TGFOU1v02.34_five_prime_utr.gtf
;	cds          	/export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii_fou.TGFOU1v02.34/genome/cds.tab
; Parsed rows per feature type
; Parsed rows per contig
;	Contig       	Total
; Host name	rsat01
; Job started	2017-02-27.073653
; Job done	2017-02-27.073726
; Seconds	0.19
;	user	0.19
;	system	0.05
;	cuser	26.73
;	csystem	5.65