; parse-gtf  -v 2 -i $RSAT/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34.gtf -fasta $RSAT/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34.pep.all.fa -org_name Plasmodium_berghei.PBANKA01.34 -task all -taxid 5823 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome
; Program version       	1.48
; Input files
;	fasta_pep    	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34.pep.all.fa
;	gtf          	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34.gtf
;	fasta_rm     	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34.dna_rm.genome.fa
;	fasta        	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34.dna.toplevel.fa
; Output files
;	three_prime_utr_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34_three_prime_utr.gtf
;	log          	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/log.txt
;	gene_start_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34_gene_start.gtf
;	stop_codon   	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/stop_codon.tab
;	tts_gtf      	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34_tts.gtf
;	peptidic_sequences	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/peptidic_sequences.fasta
;	start_codon  	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/start_codon.tab
;	fasta_rm_lengths	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34.dna_rm.genome_lengths.tab
;	gene_end_gtf 	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34_gene_end.gtf
;	exon         	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/exon.tab
;	contigs_txt  	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/contigs.txt
;	fasta_pep_lengths	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34.pep.all_lengths.tab
;	stop_codon_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34_stop_codon.gtf
;	contig_rm    	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/contig_rm.tab
;	five_prime_utr_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34_five_prime_utr.gtf
;	cds          	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/cds.tab
;	contigs_txt_rm	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/contigs_rm.txt
;	transcript_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34_transcript.gtf
;	tss_gtf      	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34_tss.gtf
;	organism     	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/organism.tab
;	contig       	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/contig.tab
;	start_codon_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34_start_codon.gtf
;	exon_gtf     	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34_exon.gtf
;	gene         	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/gene.tab
;	gene_gtf     	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34_gene.gtf
;	fasta_lengths	/export/home1/rsat/rsat/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/Plasmodium_berghei.PBANKA01.34.dna.toplevel_lengths.tab
;	transcript   	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/genome/transcript.tab
; Parsed rows per feature type
;	cds          	12968
;	exon         	13568
;	gene         	5152
;	start_codon  	4882
;	stop_codon   	4871
;	transcript   	5152
; Parsed rows per contig
;	Contig       	Total	cds	exon	gene	start	stop	transcript
;	1            	1224	349	364	130	125	126	130
;	10           	3892	1108	1133	422	404	403	422
;	11           	4247	1165	1198	480	463	461	480
;	12           	4280	1181	1202	480	469	468	480
;	13           	6337	1816	1851	676	660	658	676
;	14           	5946	1631	1648	674	660	659	674
;	2            	1560	413	488	174	156	155	174
;	3            	1571	438	465	172	163	161	172
;	4            	1750	488	516	191	183	181	191
;	5            	2380	674	704	255	246	246	255
;	6            	2306	665	674	246	239	236	246
;	7            	2264	664	689	233	223	222	233
;	8            	3405	939	960	381	372	372	381
;	9            	4340	1267	1282	455	440	441	455
;	Mt           	120	3	37	37	3	3	37
;	Pt           	198	29	37	37	29	29	37
;	berg_bin_10_43928-46895	5	1	1	1	0	1	1
;	berg_bin_11_46896-49703	10	1	4	2	0	1	2
;	berg_bin_12_49704-56537	18	5	5	2	2	2	2
;	berg_bin_13_56538-63509	20	6	6	2	2	2	2
;	berg_bin_14_63510-65707	7	2	2	1	1	0	1
;	berg_bin_15_65708-69848	5	1	1	1	1	0	1
;	berg_bin_18_76900-80115	15	4	4	2	2	1	2
;	berg_bin_19_80116-85839	10	3	3	1	1	1	1
;	berg_bin_1_1-2057	10	3	3	1	1	1	1
;	berg_bin_20_85840-92732	20	6	6	2	2	2	2
;	berg_bin_21_92733-99195	5	0	3	1	0	0	1
;	berg_bin_22_99196-101382	7	2	2	1	1	0	1
;	berg_bin_23_101383-104007	10	3	3	1	1	1	1
;	berg_bin_24_104008-106028	5	1	1	1	0	1	1
;	berg_bin_25_106029-123291	48	12	18	5	4	4	5
;	berg_bin_26_123292-125852	10	3	3	1	1	1	1
;	berg_bin_27_125853-137162	6	1	1	1	1	1	1
;	berg_bin_2_2058-9299	17	3	8	2	1	1	2
;	berg_bin_31_144424-158441	33	9	9	4	3	4	4
;	berg_bin_33_161126-167038	17	5	5	2	1	2	2
;	berg_bin_34_167039-173921	19	6	6	2	2	1	2
;	berg_bin_35_173922-179109	7	2	2	1	1	0	1
;	berg_bin_36_179110-184917	12	2	5	2	0	1	2
;	berg_bin_37_184918-190973	10	3	3	1	1	1	1
;	berg_bin_38_190974-194899	6	1	1	1	1	1	1
;	berg_bin_39_194900-197581	5	1	1	1	0	1	1
;	berg_bin_3_9300-11381	7	2	2	1	0	1	1
;	berg_bin_40_197582-203425	7	2	2	1	1	0	1
;	berg_bin_41_203426-207771	8	2	2	1	1	1	1
;	berg_bin_42_207772-224197	34	8	12	4	3	3	4
;	berg_bin_43_224198-235267	34	9	11	4	3	3	4
;	berg_bin_44_235268-245439	22	3	11	3	1	1	3
;	berg_bin_45_245440-246151	4	1	1	1	0	0	1
;	berg_bin_46_246152-248326	5	0	3	1	0	0	1
;	berg_bin_47_248327-251371	6	0	4	1	0	0	1
;	berg_bin_48_251372-253650	5	0	3	1	0	0	1
;	berg_bin_49_253651-255866	6	0	4	1	0	0	1
;	berg_bin_4_11382-18114	20	6	6	2	2	2	2
;	berg_bin_50_255867-257944	6	0	4	1	0	0	1
;	berg_bin_51_257945-260210	4	0	2	1	0	0	1
;	berg_bin_52_260211-262379	6	0	4	1	0	0	1
;	berg_bin_53_262380-264639	6	0	4	1	0	0	1
;	berg_bin_54_264640-267321	6	0	4	1	0	0	1
;	berg_bin_55_267322-269551	5	0	3	1	0	0	1
;	berg_bin_56_269552-271731	5	0	3	1	0	0	1
;	berg_bin_57_271732-273882	5	0	3	1	0	0	1
;	berg_bin_58_273883-276342	6	0	4	1	0	0	1
;	berg_bin_59_276343-278860	6	0	4	1	0	0	1
;	berg_bin_5_18115-20692	8	2	2	1	1	1	1
;	berg_bin_60_278861-280953	5	0	3	1	0	0	1
;	berg_bin_61_280954-283063	3	0	1	1	0	0	1
;	berg_bin_62_283064-285339	6	0	4	1	0	0	1
;	berg_bin_63_285340-287784	6	0	4	1	0	0	1
;	berg_bin_64_287785-289870	5	0	3	1	0	0	1
;	berg_bin_65_289871-292389	6	0	4	1	0	0	1
;	berg_bin_66_292390-294623	6	0	4	1	0	0	1
;	berg_bin_67_294624-297036	6	0	4	1	0	0	1
;	berg_bin_68_297037-300180	6	0	4	1	0	0	1
;	berg_bin_69_300181-302431	7	2	2	1	0	1	1
;	berg_bin_6_20693-23929	8	2	2	1	1	1	1
;	berg_bin_70_302432-304841	6	0	4	1	0	0	1
;	berg_bin_71_304842-307060	6	0	4	1	0	0	1
;	berg_bin_72_307061-309273	8	0	4	2	0	0	2
;	berg_bin_73_309274-311529	6	0	4	1	0	0	1
;	berg_bin_74_311530-313637	6	0	4	1	0	0	1
;	berg_bin_75_313638-316059	6	0	4	1	0	0	1
;	berg_bin_76_316060-318384	6	0	4	1	0	0	1
;	berg_bin_77_318385-320400	6	0	4	1	0	0	1
;	berg_bin_78_320401-323151	6	0	4	1	0	0	1
;	berg_bin_79_323152-325776	9	0	5	2	0	0	2
;	berg_bin_7_23930-27552	10	3	3	1	1	1	1
;	berg_bin_80_325777-328388	5	0	3	1	0	0	1
;	berg_bin_81_328389-330656	6	0	4	1	0	0	1
;	berg_bin_82_330657-334894	15	3	6	2	1	1	2
;	berg_bin_83_334895-337317	6	0	4	1	0	0	1
;	berg_bin_84_337318-339423	5	0	3	1	0	0	1
;	berg_bin_8_27553-31795	10	3	3	1	1	1	1
;	berg_bin_9_31796-43927	29	4	14	4	1	2	4
; Host name	rsat01
; Job started	2017-02-27.045108
; Job done	2017-02-27.045701
; Seconds	2.71
;	user	2.71
;	system	0.19
;	cuser	343.69
;	csystem	11.99