; parse-gtf  -v 2 -i $RSAT/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34.gtf -fasta $RSAT/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34.pep.all.fa -org_name Strongyloides_ratti.S_ratti_ED321_v5_0_4.34 -task all -taxid 34506 -gtf_source ensemblgenomes -batch -o $RSAT/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34.dna_rm.genome.fa
;	gtf          	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34.gtf
;	fasta        	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34.dna.toplevel.fa
;	fasta_pep    	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34.pep.all.fa
; Output files
;	peptidic_sequences	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/contigs_rm.txt
;	tts_gtf      	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_tts.gtf
;	gene_gtf     	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_gene.gtf
;	contig_rm    	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/contig_rm.tab
;	gene         	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/gene.tab
;	stop_codon_gtf	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_stop_codon.gtf
;	transcript   	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/transcript.tab
;	gene_start_gtf	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_gene_start.gtf
;	gene_end_gtf 	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_gene_end.gtf
;	cds          	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/cds.tab
;	three_prime_utr_gtf	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_three_prime_utr.gtf
;	log          	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/log.txt
;	exon         	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/exon.tab
;	organism     	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/organism.tab
;	contig       	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/contig.tab
;	tss_gtf      	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_tss.gtf
;	stop_codon   	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/stop_codon.tab
;	start_codon_gtf	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_start_codon.gtf
;	five_prime_utr_gtf	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_five_prime_utr.gtf
;	transcript_gtf	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_transcript.gtf
;	fasta_lengths	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34.dna.toplevel_lengths.tab
;	start_codon  	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/start_codon.tab
;	contigs_txt  	/vh/rsat/rsat/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/contigs.txt
;	fasta_pep_lengths	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34.pep.all_lengths.tab
;	fasta_rm_lengths	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34.dna_rm.genome_lengths.tab
;	exon_gtf     	/vh/rsat/rsat/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_exon.gtf
; Parsed rows per feature type
;	cds          	33960
;	exon         	34135
;	five_prime_utr	1412
;	gene         	12449
;	start_codon  	12470
;	stop_codon   	12494
;	three_prime_utr	2265
;	transcript   	12529
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	SRAE_chr1    	34675	9479	9538	481	3596	3616	3616	728	3621
;	SRAE_chr2    	51924	14157	14250	747	5365	5409	5410	1172	5414
;	SRAE_chrX_scaffold1	10602	3202	3207	48	1010	1008	1010	107	1010
;	SRAE_chrX_scaffold10	186	52	52	1	20	20	20	1	20
;	SRAE_chrX_scaffold2	8513	2542	2548	44	820	818	822	96	823
;	SRAE_chrX_scaffold3	2117	674	674	5	187	186	186	18	187
;	SRAE_chrX_scaffold4	2068	639	639	5	192	192	192	17	192
;	SRAE_chrX_scaffold5	1315	379	380	6	135	134	134	12	135
;	SRAE_chrX_scaffold6	1356	371	373	5	150	149	150	8	150
;	SRAE_chrX_scaffold7	595	183	183	1	56	56	56	4	56
;	SRAE_chrX_scaffold8	517	153	153	1	51	51	50	7	51
;	SRAE_chrX_scaffold9	128	41	41	1	11	11	11	1	11
;	SRAE_scaffold1	2820	788	790	36	290	290	289	47	290
;	SRAE_scaffold10	42	11	11	0	5	5	5	0	5
;	SRAE_scaffold101	7	2	2	0	1	1	0	0	1
;	SRAE_scaffold103	5	1	1	0	1	0	1	0	1
;	SRAE_scaffold107	5	1	1	0	1	1	0	0	1
;	SRAE_scaffold109	5	1	1	0	1	0	1	0	1
;	SRAE_scaffold12	86	21	21	0	11	11	11	0	11
;	SRAE_scaffold13	45	11	11	0	7	3	6	0	7
;	SRAE_scaffold14	23	6	6	0	3	2	3	0	3
;	SRAE_scaffold15	46	11	11	0	6	6	6	0	6
;	SRAE_scaffold16	35	8	8	0	5	4	5	0	5
;	SRAE_scaffold17	32	8	8	0	4	4	4	0	4
;	SRAE_scaffold18	50	13	13	0	6	6	6	0	6
;	SRAE_scaffold19	27	8	8	0	3	2	3	0	3
;	SRAE_scaffold2	1608	441	448	29	161	163	165	37	164
;	SRAE_scaffold20	22	5	5	0	3	3	3	0	3
;	SRAE_scaffold21	25	7	7	0	3	2	3	0	3
;	SRAE_scaffold22	13	2	2	0	2	2	2	1	2
;	SRAE_scaffold23	22	7	7	0	2	2	2	0	2
;	SRAE_scaffold24	23	6	6	0	3	2	3	0	3
;	SRAE_scaffold25	22	6	6	0	3	2	2	0	3
;	SRAE_scaffold26	10	3	3	0	1	1	1	0	1
;	SRAE_scaffold27	6	1	1	0	1	1	1	0	1
;	SRAE_scaffold28	25	7	7	0	3	2	3	0	3
;	SRAE_scaffold29	29	7	7	0	4	3	4	0	4
;	SRAE_scaffold3	963	247	247	2	116	116	116	3	116
;	SRAE_scaffold30	17	7	7	0	1	1	0	0	1
;	SRAE_scaffold31	12	4	4	0	1	1	1	0	1
;	SRAE_scaffold32	10	2	2	0	2	0	2	0	2
;	SRAE_scaffold33	14	5	5	0	1	1	1	0	1
;	SRAE_scaffold34	18	7	7	0	1	1	1	0	1
;	SRAE_scaffold35	21	7	7	0	2	2	1	0	2
;	SRAE_scaffold36	6	1	1	0	1	1	1	0	1
;	SRAE_scaffold37	14	5	5	0	1	1	1	0	1
;	SRAE_scaffold38	5	1	1	0	1	0	1	0	1
;	SRAE_scaffold39	5	1	1	0	1	0	1	0	1
;	SRAE_scaffold4	329	99	99	0	32	32	32	3	32
;	SRAE_scaffold40	11	2	2	0	2	2	1	0	2
;	SRAE_scaffold41	26	9	9	0	2	2	2	0	2
;	SRAE_scaffold42	34	11	11	0	3	2	3	1	3
;	SRAE_scaffold43	7	2	2	0	1	0	1	0	1
;	SRAE_scaffold44	4	1	1	0	1	0	0	0	1
;	SRAE_scaffold45	10	3	3	0	1	1	1	0	1
;	SRAE_scaffold46	6	1	1	0	1	1	1	0	1
;	SRAE_scaffold47	17	5	5	0	2	1	1	1	2
;	SRAE_scaffold48	15	4	4	0	2	1	2	0	2
;	SRAE_scaffold49	5	1	1	0	1	0	1	0	1
;	SRAE_scaffold5	357	91	91	0	44	44	43	0	44
;	SRAE_scaffold50	19	4	4	0	3	2	3	0	3
;	SRAE_scaffold52	12	3	3	0	2	1	1	0	2
;	SRAE_scaffold54	15	4	4	0	2	1	2	0	2
;	SRAE_scaffold56	6	1	1	0	1	1	1	0	1
;	SRAE_scaffold59	8	2	2	0	1	1	1	0	1
;	SRAE_scaffold6	228	54	54	0	30	30	30	0	30
;	SRAE_scaffold60	17	5	5	0	2	1	2	0	2
;	SRAE_scaffold61	19	5	5	0	3	2	1	0	3
;	SRAE_scaffold64	8	2	2	0	1	1	1	0	1
;	SRAE_scaffold66	7	2	2	0	1	1	0	0	1
;	SRAE_scaffold67	15	4	4	0	2	1	2	0	2
;	SRAE_scaffold68	6	1	1	0	1	1	1	0	1
;	SRAE_scaffold69	6	1	1	0	1	1	1	0	1
;	SRAE_scaffold7	122	29	29	0	16	16	16	0	16
;	SRAE_scaffold71	5	1	1	0	1	0	1	0	1
;	SRAE_scaffold73	5	1	1	0	1	1	0	0	1
;	SRAE_scaffold75	6	1	1	0	1	1	1	0	1
;	SRAE_scaffold76	4	1	1	0	1	0	0	0	1
;	SRAE_scaffold77	5	1	1	0	1	0	1	0	1
;	SRAE_scaffold78	7	2	2	0	1	1	0	0	1
;	SRAE_scaffold79	8	2	2	0	1	1	1	0	1
;	SRAE_scaffold8	79	21	21	0	9	9	9	1	9
;	SRAE_scaffold80	7	2	2	0	1	0	1	0	1
;	SRAE_scaffold82	5	1	1	0	1	1	0	0	1
;	SRAE_scaffold83	10	3	3	0	1	1	1	0	1
;	SRAE_scaffold86	8	2	2	0	1	1	1	0	1
;	SRAE_scaffold87	7	2	2	0	1	0	1	0	1
;	SRAE_scaffold88	6	1	1	0	1	1	1	0	1
;	SRAE_scaffold9	93	23	23	0	12	12	11	0	12
;	SRAE_scaffold90	11	2	2	0	2	2	1	0	2
;	SRAE_scaffold91	6	2	2	0	1	0	0	0	1
;	SRAE_scaffold92	4	1	1	0	1	0	0	0	1
;	SRAE_scaffold95	7	2	2	0	1	0	1	0	1
;	SRAE_scaffold98	8	2	2	0	1	1	1	0	1
; Host name	biow
; Job started	2017-02-26.202337
; Job done	2017-02-26.202538
; Seconds	9.72
;	user	9.72
;	system	0.99
;	cuser	101.58
;	csystem	5.52