; parse-gtf  -v 2 -i $RSAT/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40.gtf -fasta $RSAT/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40.pep.all.fa -org_name Nicotiana_attenuata.NIATTr2.40 -task all -taxid 49451 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40.dna_rm.genome.fa
;	gtf          	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40.gtf
;	fasta        	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40.dna.toplevel.fa
;	fasta_pep    	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40.pep.all.fa
; Output files
;	peptidic_sequences	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/contigs_rm.txt
;	tts_gtf      	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40_tts.gtf
;	gene_gtf     	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40_gene.gtf
;	contig_rm    	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/contig_rm.tab
;	gene         	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/gene.tab
;	stop_codon_gtf	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40_stop_codon.gtf
;	transcript   	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/transcript.tab
;	gene_start_gtf	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40_gene_start.gtf
;	gene_end_gtf 	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40_gene_end.gtf
;	cds          	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/cds.tab
;	three_prime_utr_gtf	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40_three_prime_utr.gtf
;	log          	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/log.txt
;	exon         	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/exon.tab
;	organism     	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/organism.tab
;	contig       	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/contig.tab
;	tss_gtf      	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40_tss.gtf
;	stop_codon   	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/stop_codon.tab
;	start_codon_gtf	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40_start_codon.gtf
;	five_prime_utr_gtf	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40_five_prime_utr.gtf
;	transcript_gtf	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40_transcript.gtf
;	fasta_lengths	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40.dna.toplevel_lengths.tab
;	start_codon  	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/start_codon.tab
;	contigs_txt  	/var/www/html/rsat/public_html/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/contigs.txt
;	fasta_pep_lengths	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40.pep.all_lengths.tab
;	fasta_rm_lengths	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40.dna_rm.genome_lengths.tab
;	exon_gtf     	/var/www/html/rsat/data/genomes/Nicotiana_attenuata.NIATTr2.40/genome/Nicotiana_attenuata.NIATTr2.40_exon.gtf
; Parsed rows per feature type
;	cds          	93796
;	exon         	94175
;	five_prime_utr	16440
;	gene         	21344
;	start_codon  	19375
;	stop_codon   	8062
;	three_prime_utr	16490
;	transcript   	21344
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	25629	8391	8433	1431	1804	1652	674	1440	1804
;	10           	12771	4189	4204	718	894	827	322	723	894
;	11           	12703	4195	4207	687	884	809	340	697	884
;	12           	13530	4474	4489	769	923	859	325	768	923
;	2            	24144	7948	7987	1364	1668	1524	605	1380	1668
;	3            	17950	6015	6028	987	1191	1120	420	998	1191
;	4            	4337	1379	1385	266	316	297	114	264	316
;	5            	13552	4369	4382	809	960	908	357	807	960
;	6            	20725	6694	6727	1209	1473	1355	576	1218	1473
;	7            	23484	7633	7657	1351	1664	1532	618	1365	1664
;	8            	13305	4433	4453	747	890	830	315	747	890
;	9            	10493	3451	3472	577	742	659	267	583	742
;	scaffold02061	60	22	22	2	3	3	3	2	3
;	scaffold02062	85	30	30	4	5	5	2	4	5
;	scaffold02063	38	9	9	3	4	4	2	3	4
;	scaffold02064	14	3	3	1	2	2	0	1	2
;	scaffold02066	15	5	5	1	1	1	0	1	1
;	scaffold02067	32	11	11	2	2	2	0	2	2
;	scaffold02068	18	4	4	2	2	2	0	2	2
;	scaffold02069	60	18	19	3	5	3	3	4	5
;	scaffold02070	120	47	47	5	5	5	1	5	5
;	scaffold02071	9	2	2	1	1	1	0	1	1
;	scaffold02072	21	5	5	2	2	2	1	2	2
;	scaffold02073	49	16	16	2	4	3	2	2	4
;	scaffold02075	7	2	2	0	1	1	0	0	1
;	scaffold02076	29	9	9	2	2	2	1	2	2
;	scaffold02077	16	5	5	1	1	1	1	1	1
;	scaffold02078	19	4	4	0	3	2	2	1	3
;	scaffold02079	100	32	32	7	7	7	1	7	7
;	scaffold02080	19	7	7	1	1	1	0	1	1
;	scaffold02081	23	9	9	1	1	1	0	1	1
;	scaffold02082	38	17	17	0	1	1	1	0	1
;	scaffold02083	80	29	31	3	5	3	1	3	5
;	scaffold02084	40	10	10	2	5	4	2	2	5
;	scaffold02085	62	19	19	4	5	5	1	4	5
;	scaffold02086	12	2	2	0	2	2	2	0	2
;	scaffold02087	9	2	2	1	1	1	0	1	1
;	scaffold02088	77	24	24	5	6	5	2	5	6
;	scaffold02089	66	24	25	3	4	3	0	3	4
;	scaffold02090	137	52	52	5	7	6	2	6	7
;	scaffold02091	62	18	18	5	5	4	2	5	5
;	scaffold02092	74	27	27	4	4	4	0	4	4
;	scaffold02093	66	20	20	4	5	5	3	4	5
;	scaffold02094	91	38	38	2	3	3	2	2	3
;	scaffold02095	15	5	5	1	1	1	0	1	1
;	scaffold02096	56	14	14	5	6	6	1	4	6
;	scaffold02097	32	8	9	2	4	2	1	2	4
;	scaffold02098	83	30	30	4	5	4	1	4	5
;	scaffold02099	20	5	5	1	3	2	0	1	3
;	scaffold02100	34	12	12	2	2	2	0	2	2
;	scaffold02101	65	20	20	4	5	4	2	5	5
;	scaffold02102	149	61	61	4	5	5	3	5	5
;	scaffold02103	205	87	87	5	6	6	3	5	6
;	scaffold02104	6	1	1	0	1	1	1	0	1
;	scaffold02105	157	66	66	3	5	5	4	3	5
;	scaffold02106	107	31	31	7	9	9	4	7	9
;	scaffold02107	9	2	2	1	1	1	0	1	1
;	scaffold02108	94	30	30	6	7	7	1	6	7
;	scaffold02109	68	22	22	3	5	5	2	4	5
;	scaffold02110	26	8	8	2	2	2	0	2	2
;	scaffold02111	167	56	56	10	11	11	2	10	11
;	scaffold02112	159	64	65	5	6	5	3	5	6
;	scaffold02114	105	40	40	5	5	5	0	5	5
;	scaffold02118	24	7	7	2	2	2	0	2	2
;	scaffold02119	45	16	16	2	3	2	1	2	3
;	scaffold02121	31	11	11	1	2	1	2	1	2
;	scaffold02123	46	18	18	1	2	2	2	1	2
;	scaffold02124	6	1	1	0	1	1	1	0	1
;	scaffold02125	31	5	5	1	5	5	4	1	5
;	scaffold02126	128	43	43	8	8	8	2	8	8
;	scaffold02127	26	8	8	1	2	2	2	1	2
;	scaffold02128	36	10	10	3	3	3	1	3	3
;	scaffold02129	72	22	22	5	6	5	1	5	6
;	scaffold02130	69	27	27	2	3	3	2	2	3
;	scaffold02131	61	20	20	4	4	4	1	4	4
;	scaffold02132	21	5	5	2	2	2	1	2	2
;	scaffold02133	57	16	16	4	5	5	2	4	5
;	scaffold02134	49	17	17	3	3	3	0	3	3
;	scaffold02135	62	18	18	5	5	5	1	5	5
;	scaffold02136	49	16	16	3	3	3	2	3	3
;	scaffold02137	9	2	2	1	1	1	0	1	1
;	scaffold02138	93	30	30	6	6	6	3	6	6
;	scaffold02139	88	30	30	5	5	5	3	5	5
;	scaffold02140	54	16	16	4	4	4	2	4	4
;	scaffold02141	58	20	20	3	3	3	3	3	3
;	scaffold02142	52	19	19	2	3	3	1	2	3
;	scaffold02143	20	6	6	1	2	1	1	1	2
;	scaffold02144	42	11	11	4	4	4	0	4	4
;	scaffold02145	61	21	21	3	4	4	1	3	4
;	scaffold02146	15	3	3	1	2	2	1	1	2
;	scaffold02147	35	8	9	3	4	3	1	3	4
;	scaffold02148	74	24	24	5	5	5	1	5	5
;	scaffold02149	19	6	6	0	2	2	1	0	2
;	scaffold02150	23	5	5	2	3	3	0	2	3
;	scaffold02151	23	4	4	2	3	3	1	3	3
;	scaffold02152	19	5	5	1	2	1	2	1	2
;	scaffold02153	61	16	17	3	7	6	2	3	7
;	scaffold02154	19	7	7	1	1	1	0	1	1
;	scaffold02155	41	13	13	2	3	3	2	2	3
;	scaffold02156	63	24	24	3	3	3	0	3	3
;	scaffold02157	13	4	4	1	1	1	0	1	1
;	scaffold02158	15	4	4	1	2	1	0	1	2
;	scaffold02159	30	9	9	2	2	2	2	2	2
;	scaffold02160	18	3	3	1	3	3	1	1	3
;	scaffold02161	38	14	14	2	2	2	0	2	2
;	scaffold02162	56	17	17	4	4	4	2	4	4
;	scaffold02163	25	7	7	2	2	2	1	2	2
;	scaffold02164	36	8	8	1	5	5	3	1	5
;	scaffold02165	22	6	8	0	3	1	0	1	3
;	scaffold02166	18	4	4	2	2	2	0	2	2
;	scaffold02167	12	3	3	1	1	1	1	1	1
;	scaffold02168	30	11	11	1	2	2	0	1	2
;	scaffold02169	118	41	41	6	7	7	3	6	7
;	scaffold02170	7	1	1	1	1	1	0	1	1
;	scaffold02171	69	24	24	4	4	4	1	4	4
;	scaffold02172	4	1	1	0	1	0	0	0	1
;	scaffold02173	50	12	12	4	6	4	2	4	6
;	scaffold02174	35	11	11	2	3	2	1	2	3
;	scaffold02175	8	2	2	0	1	1	1	0	1
;	scaffold02176	20	5	5	2	2	2	0	2	2
;	scaffold02177	79	29	29	4	4	4	1	4	4
;	scaffold02178	78	29	29	4	4	4	0	4	4
;	scaffold02179	9	2	2	1	1	1	0	1	1
;	scaffold02180	99	35	36	5	6	5	1	5	6
;	scaffold02182	85	30	30	4	5	5	2	4	5
;	scaffold02183	81	23	23	5	7	6	5	5	7
;	scaffold02185	62	20	21	3	5	4	1	3	5
;	scaffold02186	35	7	7	3	4	4	3	3	4
;	scaffold02187	13	4	4	1	1	1	0	1	1
;	scaffold02188	22	5	5	1	3	2	2	1	3
;	scaffold02189	28	11	11	1	1	1	1	1	1
;	scaffold02190	69	22	22	4	5	4	3	4	5
;	scaffold02191	11	3	3	1	1	1	0	1	1
;	scaffold02192	11	3	3	1	1	1	0	1	1
;	scaffold02193	95	26	26	6	9	8	5	6	9
;	scaffold02194	38	14	14	2	2	2	0	2	2
;	scaffold02195	94	24	24	7	9	9	5	7	9
;	scaffold02197	82	26	26	6	6	6	0	6	6
;	scaffold02198	28	6	6	2	4	3	1	2	4
;	scaffold02199	107	35	35	6	7	7	4	6	7
;	scaffold02200	22	6	6	2	2	2	0	2	2
;	scaffold02202	9	2	2	1	1	1	0	1	1
;	scaffold02203	10	2	2	0	2	2	0	0	2
;	scaffold02204	49	13	13	4	4	4	3	4	4
;	scaffold02205	58	19	19	3	4	4	2	3	4
;	scaffold02206	73	27	27	3	4	4	1	3	4
;	scaffold02207	14	3	3	1	2	2	0	1	2
;	scaffold02208	39	12	12	2	3	3	2	2	3
;	scaffold02209	76	28	28	4	4	4	0	4	4
;	scaffold02210	9	2	2	0	2	0	1	0	2
;	scaffold02211	6	1	1	0	1	1	0	1	1
;	scaffold02212	40	9	9	4	4	4	3	3	4
;	scaffold02213	18	4	4	2	2	2	0	2	2
;	scaffold02214	16	3	3	1	2	2	2	1	2
;	scaffold02215	54	16	16	4	4	4	2	4	4
;	scaffold02216	50	17	17	3	3	3	1	3	3
;	scaffold02217	75	32	32	2	2	2	1	2	2
;	scaffold02218	65	18	18	4	6	5	4	4	6
;	scaffold02219	45	16	16	2	3	2	1	2	3
;	scaffold02221	16	3	3	1	2	2	2	1	2
;	scaffold02222	7	1	1	1	1	1	0	1	1
;	scaffold02223	72	26	26	3	4	4	2	3	4
;	scaffold02224	83	22	23	6	8	7	3	6	8
;	scaffold02225	135	42	42	10	10	10	1	10	10
;	scaffold02227	56	22	22	2	2	2	2	2	2
;	scaffold02228	11	3	3	1	1	1	0	1	1
;	scaffold02229	29	11	11	1	2	1	0	1	2
;	scaffold02230	48	22	22	0	1	1	0	1	1
;	scaffold02231	9	2	2	1	1	1	0	1	1
;	scaffold02232	40	15	15	2	2	2	0	2	2
;	scaffold02233	8	1	1	1	1	1	1	1	1
;	scaffold02234	101	41	41	3	4	3	2	3	4
;	scaffold02235	130	45	46	6	8	7	4	6	8
;	scaffold02236	42	14	14	2	3	3	1	2	3
;	scaffold02237	11	3	3	1	1	1	0	1	1
;	scaffold02238	19	6	6	1	2	1	0	1	2
;	scaffold02240	13	4	4	1	1	1	0	1	1
;	scaffold02241	101	35	35	5	6	6	3	5	6
;	scaffold02243	38	9	9	3	5	4	0	3	5
;	scaffold02244	15	4	4	0	2	2	1	0	2
;	scaffold02245	22	6	6	2	2	2	0	2	2
;	scaffold02246	15	3	3	1	2	2	1	1	2
;	scaffold02248	85	29	29	5	5	5	2	5	5
;	scaffold02250	18	6	6	1	1	1	1	1	1
;	scaffold02252	39	10	10	3	4	4	1	3	4
;	scaffold02253	40	9	9	4	4	4	2	4	4
;	scaffold02254	94	39	39	3	3	3	1	3	3
;	scaffold02255	38	7	7	4	5	5	2	3	5
;	scaffold02257	39	11	11	2	4	3	2	2	4
;	scaffold02258	39	9	9	4	4	4	1	4	4
;	scaffold02259	57	10	10	6	8	8	1	6	8
;	scaffold02260	9	2	2	1	1	1	0	1	1
;	scaffold02261	42	16	16	1	2	2	2	1	2
;	scaffold02262	85	30	30	4	5	5	2	4	5
;	scaffold02263	66	27	27	0	3	3	3	0	3
;	scaffold02264	41	12	12	3	3	3	2	3	3
;	scaffold02265	78	21	22	6	7	6	3	6	7
;	scaffold02266	79	25	25	5	6	6	1	5	6
;	scaffold02267	63	21	21	3	4	4	3	3	4
;	scaffold02268	22	6	6	2	2	2	0	2	2
;	scaffold02269	21	5	5	2	2	2	1	2	2
;	scaffold02270	37	11	11	2	3	3	2	2	3
;	scaffold02271	46	10	10	5	5	5	1	5	5
;	scaffold02272	17	4	4	1	2	2	1	1	2
;	scaffold02273	14	6	6	0	1	0	0	0	1
;	scaffold02274	38	11	11	3	3	3	1	3	3
;	scaffold02275	55	20	20	3	3	3	0	3	3
;	scaffold02276	7	1	1	1	1	1	0	1	1
;	scaffold02277	49	17	17	3	3	3	0	3	3
;	scaffold02278	58	15	15	5	5	5	3	5	5
;	scaffold02279	14	2	2	2	2	2	0	2	2
;	scaffold02280	101	42	42	3	3	3	2	3	3
;	scaffold02281	22	8	8	1	1	1	1	1	1
;	scaffold02285	43	11	11	4	4	4	1	4	4
;	scaffold02286	32	10	10	2	2	2	2	2	2
;	scaffold02287	7	1	1	1	1	1	0	1	1
;	scaffold02288	17	4	4	1	2	2	1	1	2
;	scaffold02289	7	1	1	1	1	1	0	1	1
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; Host name	baobab.eead.csic.es
; Job started	2018-09-20.174214
; Job done	2018-09-21.052459
; Seconds	120.99
;	user	120.99
;	system	140.44
;	cuser	40582.33
;	csystem	1260.16