; parse-gtf  -v 2 -i $RSAT/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34.gtf -fasta $RSAT/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34.pep.all.fa -org_name Drosophila_melanogaster.BDGP6.34 -task all -taxid 7227 -gtf_source ensemblgenomes -batch -o $RSAT/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34.dna_rm.genome.fa
;	gtf          	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34.gtf
;	fasta        	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34.dna.toplevel.fa
;	fasta_pep    	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34.pep.all.fa
; Output files
;	peptidic_sequences	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/peptidic_sequences.fasta
;	contigs_txt_rm	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/contigs_rm.txt
;	tts_gtf      	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34_tts.gtf
;	gene_gtf     	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34_gene.gtf
;	contig_rm    	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/contig_rm.tab
;	gene         	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/gene.tab
;	stop_codon_gtf	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34_stop_codon.gtf
;	transcript   	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/transcript.tab
;	gene_start_gtf	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34_gene_start.gtf
;	gene_end_gtf 	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34_gene_end.gtf
;	cds          	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/cds.tab
;	three_prime_utr_gtf	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34_three_prime_utr.gtf
;	log          	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/log.txt
;	exon         	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/exon.tab
;	organism     	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/organism.tab
;	contig       	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/contig.tab
;	tss_gtf      	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34_tss.gtf
;	stop_codon   	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/stop_codon.tab
;	start_codon_gtf	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34_start_codon.gtf
;	five_prime_utr_gtf	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34_five_prime_utr.gtf
;	transcript_gtf	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34_transcript.gtf
;	fasta_lengths	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34.dna.toplevel_lengths.tab
;	start_codon  	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/start_codon.tab
;	contigs_txt  	/vh/rsat/rsat/public_html/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/contigs.txt
;	fasta_pep_lengths	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34.pep.all_lengths.tab
;	fasta_rm_lengths	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34.dna_rm.genome_lengths.tab
;	exon_gtf     	/vh/rsat/rsat/data/genomes/Drosophila_melanogaster.BDGP6.34/genome/Drosophila_melanogaster.BDGP6.34_exon.gtf
; Parsed rows per feature type
;	cds          	160188
;	exon         	186414
;	five_prime_utr	46060
;	gene         	17559
;	selenocysteine	4
;	start_codon  	30389
;	stop_codon   	30296
;	three_prime_utr	33034
;	transcript   	34740
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	selenocysteine	start	stop	three_prime_utr	transcript
;	211000022278158	3	0	1	0	1	0	0	0	0	1
;	211000022278279	3	0	1	0	1	0	0	0	0	1
;	211000022278282	3	0	1	0	1	0	0	0	0	1
;	211000022278298	3	0	1	0	1	0	0	0	0	1
;	211000022278307	3	0	1	0	1	0	0	0	0	1
;	211000022278309	3	0	1	0	1	0	0	0	0	1
;	211000022278436	3	0	1	0	1	0	0	0	0	1
;	211000022278449	4	0	2	0	1	0	0	0	0	1
;	211000022278498	3	0	1	0	1	0	0	0	0	1
;	211000022278522	3	0	1	0	1	0	0	0	0	1
;	211000022278603	3	0	1	0	1	0	0	0	0	1
;	211000022278604	3	0	1	0	1	0	0	0	0	1
;	211000022278664	3	0	1	0	1	0	0	0	0	1
;	211000022278724	3	0	1	0	1	0	0	0	0	1
;	211000022278750	3	0	1	0	1	0	0	0	0	1
;	211000022278760	7	2	2	0	1	0	1	0	0	1
;	211000022278875	3	0	1	0	1	0	0	0	0	1
;	211000022278877	3	0	1	0	1	0	0	0	0	1
;	211000022278878	3	0	1	0	1	0	0	0	0	1
;	211000022278879	3	0	1	0	1	0	0	0	0	1
;	211000022278880	3	0	1	0	1	0	0	0	0	1
;	211000022278985	3	0	1	0	1	0	0	0	0	1
;	211000022279055	3	0	1	0	1	0	0	0	0	1
;	211000022279108	3	0	1	0	1	0	0	0	0	1
;	211000022279132	3	0	1	0	1	0	0	0	0	1
;	211000022279134	3	0	1	0	1	0	0	0	0	1
;	211000022279165	3	0	1	0	1	0	0	0	0	1
;	211000022279188	12	3	3	1	1	0	1	1	1	1
;	211000022279222	3	0	1	0	1	0	0	0	0	1
;	211000022279264	3	0	1	0	1	0	0	0	0	1
;	211000022279342	3	0	1	0	1	0	0	0	0	1
;	211000022279392	3	0	1	0	1	0	0	0	0	1
;	211000022279446	3	0	1	0	1	0	0	0	0	1
;	211000022279528	3	0	1	0	1	0	0	0	0	1
;	211000022279529	3	0	1	0	1	0	0	0	0	1
;	211000022279531	3	0	1	0	1	0	0	0	0	1
;	211000022279555	3	0	1	0	1	0	0	0	0	1
;	211000022279681	3	0	1	0	1	0	0	0	0	1
;	211000022279708	3	0	1	0	1	0	0	0	0	1
;	211000022280133	3	0	1	0	1	0	0	0	0	1
;	211000022280328	14	4	4	1	1	0	1	1	1	1
;	211000022280341	3	0	1	0	1	0	0	0	0	1
;	211000022280347	3	0	1	0	1	0	0	0	0	1
;	211000022280481	3	0	1	0	1	0	0	0	0	1
;	211000022280494	6	0	2	0	2	0	0	0	0	2
;	211000022280645	3	0	1	0	1	0	0	0	0	1
;	211000022280703	3	0	1	0	1	0	0	0	0	1
;	2L           	96740	28047	32747	8374	3465	2	5675	5656	6142	6632
;	2R           	110108	33657	38551	8842	3601	0	6028	6018	6484	6927
;	3L           	100745	29473	34347	8738	3433	0	5873	5853	6352	6676
;	3R           	125133	37167	43159	10693	4125	0	7105	7092	7782	8010
;	4            	7844	2732	3165	570	111	0	295	289	339	343
;	Unmapped_Scaffold_8	43	12	14	4	2	0	3	3	2	3
;	X            	97193	28967	34136	8824	2647	2	5372	5351	5921	5973
;	Y            	504	111	182	13	71	0	23	22	10	72
;	dmel_mitochondrion_genome	146	13	37	0	37	0	12	10	0	37
;	rDNA         	59	0	21	0	19	0	0	0	0	19
; Host name	biow
; Job started	2017-02-26.163808
; Job done	2017-02-26.164236
; Seconds	35.7
;	user	35.7
;	system	7.37
;	cuser	209.51
;	csystem	11.73