; parse-gtf  -v 2 -i $RSAT/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34.gtf -fasta $RSAT/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34.pep.all.fa -org_name Plasmodium_knowlesi.ASM635v1.34 -task all -taxid 5851 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34.dna_rm.genome.fa
;	fasta        	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34.dna.toplevel.fa
;	fasta_pep    	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34.pep.all.fa
;	gtf          	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34.gtf
; Output files
;	start_codon  	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/start_codon.tab
;	log          	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/log.txt
;	stop_codon_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34_stop_codon.gtf
;	tts_gtf      	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34_tts.gtf
;	tss_gtf      	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34_tss.gtf
;	gene_end_gtf 	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34_gene_end.gtf
;	contigs_txt_rm	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/contigs_rm.txt
;	contigs_txt  	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/contigs.txt
;	gene_gtf     	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34_gene.gtf
;	peptidic_sequences	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/peptidic_sequences.fasta
;	contig_rm    	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/contig_rm.tab
;	transcript   	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/transcript.tab
;	exon         	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/exon.tab
;	fasta_pep_lengths	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34.pep.all_lengths.tab
;	stop_codon   	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/stop_codon.tab
;	five_prime_utr_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34_five_prime_utr.gtf
;	gene         	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/gene.tab
;	three_prime_utr_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34_three_prime_utr.gtf
;	cds          	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/cds.tab
;	exon_gtf     	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34_exon.gtf
;	transcript_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34_transcript.gtf
;	fasta_lengths	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34.dna.toplevel_lengths.tab
;	contig       	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/contig.tab
;	start_codon_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34_start_codon.gtf
;	fasta_rm_lengths	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34.dna_rm.genome_lengths.tab
;	organism     	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/organism.tab
;	gene_start_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_knowlesi.ASM635v1.34/genome/Plasmodium_knowlesi.ASM635v1.34_gene_start.gtf
; Parsed rows per feature type
;	cds          	13296
;	exon         	13459
;	five_prime_utr	35
;	gene         	5258
;	start_codon  	4976
;	stop_codon   	5005
;	transcript   	5258
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	transcript
;	1            	1534	388	408	0	195	173	175	195
;	10           	2941	809	825	3	336	315	317	336
;	11           	4677	1339	1357	6	509	476	481	509
;	12           	6591	1860	1880	3	727	695	699	727
;	13           	4331	1232	1243	2	475	448	456	475
;	14           	6140	1674	1689	1	707	682	680	707
;	2            	1485	421	426	0	165	153	155	165
;	3            	1955	550	570	1	220	198	196	220
;	4            	1709	490	498	4	185	173	174	185
;	5            	2718	782	790	0	295	279	277	295
;	6            	2186	627	628	2	235	229	230	235
;	7            	3210	923	923	4	343	337	337	343
;	8            	3473	962	971	7	394	370	375	394
;	9            	4337	1239	1251	2	472	448	453	472
; Host name	rsat01
; Job started	2017-02-27.052113
; Job done	2017-02-27.052726
; Seconds	3.07
;	user	3.07
;	system	0.16
;	cuser	362.13
;	csystem	12.37