; parse-gtf  -v 2 -i $RSAT/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34.gtf -fasta $RSAT/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34.pep.all.fa -org_name Pythium_aphanidermatum.pag1_scaffolds_v1.34 -task all -taxid 1223555 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome
; Program version       	1.48
; Input files
;	fasta_pep    	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34.pep.all.fa
;	fasta        	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34.dna.toplevel.fa
;	fasta_rm     	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34.dna_rm.genome.fa
;	gtf          	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34.gtf
; Output files
;	stop_codon   	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/stop_codon.tab
;	stop_codon_gtf	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34_stop_codon.gtf
;	start_codon  	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/start_codon.tab
;	contig       	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/contig.tab
;	gene_gtf     	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34_gene.gtf
;	gene_start_gtf	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34_gene_start.gtf
;	contig_rm    	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/contig_rm.tab
;	three_prime_utr_gtf	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34_three_prime_utr.gtf
;	tts_gtf      	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34_tts.gtf
;	tss_gtf      	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34_tss.gtf
;	peptidic_sequences	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/peptidic_sequences.fasta
;	log          	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/log.txt
;	gene         	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/gene.tab
;	fasta_lengths	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34.dna.toplevel_lengths.tab
;	organism     	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/organism.tab
;	gene_end_gtf 	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34_gene_end.gtf
;	transcript_gtf	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34_transcript.gtf
;	exon_gtf     	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34_exon.gtf
;	contigs_txt  	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/contigs.txt
;	cds          	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/cds.tab
;	start_codon_gtf	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34_start_codon.gtf
;	contigs_txt_rm	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/contigs_rm.txt
;	exon         	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/exon.tab
;	fasta_pep_lengths	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34.pep.all_lengths.tab
;	transcript   	/export/home1/rsat/rsat/public_html/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/transcript.tab
;	fasta_rm_lengths	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34.dna_rm.genome_lengths.tab
;	five_prime_utr_gtf	/export/home1/rsat/rsat/data/genomes/Pythium_aphanidermatum.pag1_scaffolds_v1.34/genome/Pythium_aphanidermatum.pag1_scaffolds_v1.34_five_prime_utr.gtf
; Parsed rows per feature type
;	cds          	28726
;	exon         	28791
;	five_prime_utr	687
;	gene         	12363
;	start_codon  	11731
;	stop_codon   	10930
;	three_prime_utr	561
;	transcript   	12370
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	pag1_scaffold_1	749	205	208	2	87	80	78	2	87
;	pag1_scaffold_10	420	117	117	1	47	47	43	1	47
;	pag1_scaffold_100	254	80	80	1	24	22	22	1	24
;	pag1_scaffold_1000	36	8	8	0	5	5	5	0	5
;	pag1_scaffold_1001	12	4	4	0	1	1	1	0	1
;	pag1_scaffold_1002	27	8	8	1	3	2	1	1	3
;	pag1_scaffold_1003	36	10	10	0	4	4	4	0	4
;	pag1_scaffold_1004	24	6	6	0	3	3	3	0	3
;	pag1_scaffold_1005	11	2	2	0	2	2	1	0	2
;	pag1_scaffold_1006	20	4	4	0	3	3	3	0	3
;	pag1_scaffold_1007	20	6	6	0	2	2	2	0	2
;	pag1_scaffold_1008	12	2	2	0	2	2	2	0	2
;	pag1_scaffold_101	197	48	48	5	25	21	21	4	25
;	pag1_scaffold_1010	32	8	8	1	4	3	3	1	4
;	pag1_scaffold_1011	33	9	9	0	4	4	3	0	4
;	pag1_scaffold_1013	38	8	8	0	6	4	6	0	6
;	pag1_scaffold_1014	18	3	3	0	3	3	3	0	3
;	pag1_scaffold_1015	28	8	8	0	3	3	3	0	3
;	pag1_scaffold_1016	12	4	4	0	1	1	1	0	1
;	pag1_scaffold_1017	24	6	6	0	3	3	3	0	3
;	pag1_scaffold_1018	8	2	2	0	1	1	1	0	1
;	pag1_scaffold_1019	28	6	6	0	4	4	4	0	4
;	pag1_scaffold_102	205	62	62	2	20	19	18	2	20
;	pag1_scaffold_1020	26	7	7	0	3	3	3	0	3
;	pag1_scaffold_1021	19	6	6	0	2	1	2	0	2
;	pag1_scaffold_1022	19	6	6	0	2	2	1	0	2
;	pag1_scaffold_1024	61	21	21	1	5	4	3	1	5
;	pag1_scaffold_1025	48	13	13	0	6	5	5	0	6
;	pag1_scaffold_1026	23	6	6	0	3	3	2	0	3
;	pag1_scaffold_1027	23	5	5	1	3	3	3	0	3
;	pag1_scaffold_1028	28	6	6	1	4	3	3	1	4
;	pag1_scaffold_1029	6	1	1	0	1	1	1	0	1
;	pag1_scaffold_103	207	58	58	3	23	22	17	3	23
;	pag1_scaffold_1030	32	8	8	0	4	4	4	0	4
;	pag1_scaffold_1032	24	4	4	1	4	4	3	0	4
;	pag1_scaffold_1033	12	2	2	0	2	2	2	0	2
;	pag1_scaffold_1034	13	2	2	1	2	2	2	0	2
;	pag1_scaffold_1035	18	5	5	1	2	1	1	1	2
;	pag1_scaffold_1036	12	2	2	0	2	2	2	0	2
;	pag1_scaffold_1037	15	4	4	0	2	1	2	0	2
;	pag1_scaffold_1038	11	2	2	0	2	2	1	0	2
;	pag1_scaffold_1039	34	7	7	0	5	5	5	0	5
;	pag1_scaffold_104	255	83	83	1	22	22	22	0	22
;	pag1_scaffold_1040	30	9	9	1	3	2	2	1	3
;	pag1_scaffold_1041	6	1	1	0	1	1	1	0	1
;	pag1_scaffold_1042	23	6	6	0	3	3	2	0	3
;	pag1_scaffold_1043	32	6	6	1	5	4	4	1	5
;	pag1_scaffold_1044	22	5	5	0	3	3	3	0	3
;	pag1_scaffold_1045	35	10	10	0	4	4	3	0	4
;	pag1_scaffold_1046	8	2	2	0	1	1	1	0	1
;	pag1_scaffold_1047	12	2	2	1	2	1	1	1	2
;	pag1_scaffold_1048	14	3	3	0	2	2	2	0	2
;	pag1_scaffold_1049	24	6	6	0	3	3	3	0	3
;	pag1_scaffold_105	223	67	67	1	22	22	21	1	22
;	pag1_scaffold_1050	39	12	12	0	4	4	3	0	4
;	pag1_scaffold_1051	16	4	4	0	2	2	2	0	2
;	pag1_scaffold_1052	26	7	7	0	3	3	3	0	3
;	pag1_scaffold_1054	27	6	6	0	4	4	3	0	4
;	pag1_scaffold_1055	18	5	5	0	2	2	2	0	2
;	pag1_scaffold_1056	8	2	2	0	1	1	1	0	1
;	pag1_scaffold_1057	17	3	3	0	3	3	2	0	3
;	pag1_scaffold_1059	16	4	4	0	2	2	2	0	2
;	pag1_scaffold_106	194	49	49	0	24	24	24	0	24
;	pag1_scaffold_1061	28	6	6	0	4	4	4	0	4
;	pag1_scaffold_1062	21	4	4	1	3	3	2	1	3
;	pag1_scaffold_1063	12	4	4	0	1	1	1	0	1
;	pag1_scaffold_1064	11	4	4	0	1	1	0	0	1
;	pag1_scaffold_1065	21	4	4	1	3	3	3	0	3
;	pag1_scaffold_1066	6	1	1	0	1	1	1	0	1
;	pag1_scaffold_1067	18	3	3	0	3	3	3	0	3
;	pag1_scaffold_1068	22	5	5	0	3	3	3	0	3
;	pag1_scaffold_1069	31	11	11	1	2	2	2	0	2
;	pag1_scaffold_107	305	88	88	1	32	32	30	1	33
;	pag1_scaffold_1070	20	6	6	0	2	2	2	0	2
;	pag1_scaffold_1071	20	6	6	1	2	1	1	1	2
;	pag1_scaffold_1072	14	3	3	1	2	1	1	1	2
;	pag1_scaffold_1074	25	9	9	0	2	2	1	0	2
;	pag1_scaffold_1075	5	1	1	0	1	1	0	0	1
;	pag1_scaffold_1078	43	14	14	0	4	4	3	0	4
;	pag1_scaffold_1079	33	9	9	0	4	4	3	0	4
;	pag1_scaffold_108	163	44	44	0	19	19	18	0	19
;	pag1_scaffold_1080	16	6	6	0	1	1	1	0	1
;	pag1_scaffold_1082	53	15	15	0	6	5	6	0	6
;	pag1_scaffold_1083	6	1	1	1	1	0	0	1	1
;	pag1_scaffold_1084	26	5	5	1	4	3	3	1	4
;	pag1_scaffold_1085	20	4	4	0	3	3	3	0	3
;	pag1_scaffold_1086	6	0	2	0	2	0	0	0	2
;	pag1_scaffold_1087	26	7	7	1	3	2	2	1	3
;	pag1_scaffold_1088	24	6	6	0	3	3	3	0	3
;	pag1_scaffold_1089	12	2	2	0	2	2	2	0	2
;	pag1_scaffold_109	166	47	47	0	18	18	18	0	18
;	pag1_scaffold_1090	5	1	1	0	1	1	0	0	1
;	pag1_scaffold_1091	31	8	8	0	4	4	3	0	4
;	pag1_scaffold_1092	12	4	4	0	1	1	1	0	1
;	pag1_scaffold_1093	22	7	7	0	2	2	2	0	2
;	pag1_scaffold_1094	27	5	5	2	4	3	3	1	4
;	pag1_scaffold_1095	22	5	5	0	3	3	3	0	3
;	pag1_scaffold_1096	21	4	4	1	3	3	3	0	3
;	pag1_scaffold_1097	20	4	4	1	3	2	2	1	3
;	pag1_scaffold_1098	10	3	3	1	1	0	0	1	1
;	pag1_scaffold_11	325	100	100	0	32	31	30	0	32
;	pag1_scaffold_110	113	27	27	0	15	15	14	0	15
;	pag1_scaffold_1100	16	4	4	0	2	2	2	0	2
;	pag1_scaffold_1101	26	5	5	0	4	4	4	0	4
;	pag1_scaffold_1102	26	7	7	0	3	3	3	0	3
;	pag1_scaffold_1103	12	2	2	0	2	2	2	0	2
;	pag1_scaffold_1104	23	7	7	0	3	2	1	0	3
;	pag1_scaffold_1105	29	6	6	1	4	4	3	1	4
;	pag1_scaffold_1106	17	4	4	1	2	2	1	1	2
;	pag1_scaffold_1107	42	10	10	0	6	5	5	0	6
;	pag1_scaffold_1108	26	5	5	0	4	4	4	0	4
;	pag1_scaffold_1109	5	1	1	0	1	1	0	0	1
;	pag1_scaffold_111	170	40	40	0	23	22	22	0	23
;	pag1_scaffold_1110	19	4	4	0	3	3	2	0	3
;	pag1_scaffold_1111	29	6	6	2	4	3	2	2	4
;	pag1_scaffold_1112	16	4	4	0	2	2	2	0	2
;	pag1_scaffold_1114	20	4	4	0	3	3	3	0	3
;	pag1_scaffold_1115	18	4	4	0	3	2	2	0	3
;	pag1_scaffold_1116	10	3	3	0	1	1	1	0	1
;	pag1_scaffold_1117	11	2	2	0	2	2	1	0	2
;	pag1_scaffold_1118	12	4	4	0	1	1	1	0	1
;	pag1_scaffold_1119	12	2	2	1	2	1	1	1	2
;	pag1_scaffold_112	148	34	34	2	20	18	18	2	20
;	pag1_scaffold_1120	31	8	8	1	4	3	2	1	4
;	pag1_scaffold_1121	21	5	5	0	3	2	3	0	3
;	pag1_scaffold_1122	18	3	3	0	3	3	3	0	3
;	pag1_scaffold_1123	16	6	6	0	1	1	1	0	1
;	pag1_scaffold_1124	26	7	7	0	3	3	3	0	3
;	pag1_scaffold_1125	24	6	6	0	3	3	3	0	3
;	pag1_scaffold_1126	12	2	2	0	2	2	2	0	2
;	pag1_scaffold_1127	6	1	1	0	1	1	1	0	1
;	pag1_scaffold_1128	5	1	1	0	1	1	0	0	1
;	pag1_scaffold_1129	18	3	3	0	3	3	3	0	3
;	pag1_scaffold_113	138	34	34	1	18	17	15	1	18
;	pag1_scaffold_1131	24	8	8	0	2	2	2	0	2
;	pag1_scaffold_1132	13	3	3	0	2	2	1	0	2
;	pag1_scaffold_1133	22	5	5	0	3	3	3	0	3
;	pag1_scaffold_1134	24	6	6	1	3	2	2	1	3
;	pag1_scaffold_1135	33	7	7	0	5	5	4	0	5
;	pag1_scaffold_1136	16	3	3	0	3	3	1	0	3
;	pag1_scaffold_1137	27	6	6	0	4	4	3	0	4
;	pag1_scaffold_1138	11	4	4	0	1	1	0	0	1
;	pag1_scaffold_1139	8	2	2	0	1	1	1	0	1
;	pag1_scaffold_114	173	44	44	1	22	21	18	1	22
;	pag1_scaffold_1140	13	3	3	0	2	2	1	0	2
;	pag1_scaffold_1143	28	10	10	0	2	2	2	0	2
;	pag1_scaffold_1144	11	2	2	0	2	2	1	0	2
;	pag1_scaffold_1145	12	2	2	0	2	2	2	0	2
;	pag1_scaffold_1146	11	2	2	0	2	2	1	0	2
;	pag1_scaffold_1147	6	1	1	0	1	1	1	0	1
;	pag1_scaffold_1148	18	5	5	0	2	2	2	0	2
;	pag1_scaffold_1149	30	9	9	0	3	3	3	0	3
;	pag1_scaffold_115	264	75	75	0	29	29	27	0	29
;	pag1_scaffold_1150	22	5	5	0	3	3	3	0	3
;	pag1_scaffold_1151	19	6	7	0	2	1	1	0	2
;	pag1_scaffold_1152	22	8	8	0	2	2	0	0	2
;	pag1_scaffold_1153	5	1	1	0	1	1	0	0	1
;	pag1_scaffold_1154	12	2	2	1	2	2	0	1	2
;	pag1_scaffold_1156	19	4	4	0	3	3	2	0	3
;	pag1_scaffold_1157	6	1	1	1	1	0	0	1	1
;	pag1_scaffold_1158	24	7	7	0	3	3	1	0	3
;	pag1_scaffold_1159	32	6	6	1	5	4	5	0	5
;	pag1_scaffold_116	182	48	48	2	22	19	20	1	22
;	pag1_scaffold_1160	17	3	3	0	3	3	2	0	3
;	pag1_scaffold_1161	18	3	3	0	3	3	3	0	3
;	pag1_scaffold_1163	11	2	2	0	2	1	2	0	2
;	pag1_scaffold_1164	11	2	2	0	2	2	1	0	2
;	pag1_scaffold_1165	16	4	4	0	2	2	2	0	2
;	pag1_scaffold_1166	10	3	3	0	1	1	1	0	1
;	pag1_scaffold_1167	24	4	7	1	5	1	0	1	5
;	pag1_scaffold_1168	14	3	3	0	2	2	2	0	2
;	pag1_scaffold_1169	28	6	6	0	4	4	4	0	4
;	pag1_scaffold_117	164	43	43	1	20	20	16	1	20
;	pag1_scaffold_1170	19	4	4	0	3	2	3	0	3
;	pag1_scaffold_1171	14	3	3	0	2	2	2	0	2
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; Host name	rsat01
; Job started	2017-02-27.054127
; Job done	2017-02-27.055141
; Seconds	6
;	user	6
;	system	0.4
;	cuser	596.82
;	csystem	15.82