; parse-gtf -v 2 -i $RSAT/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40.gtf -fasta $RSAT/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40.pep.all.fa -org_name Setaria_italica.Setaria_italica_v2.0.40 -task all -taxid 4555 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome ; Program version 1.48 ; Input files ; fasta_rm /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40.dna_rm.genome.fa ; gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40.gtf ; fasta /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40.dna.toplevel.fa ; fasta_pep /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40.pep.all.fa ; Output files ; peptidic_sequences /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/peptidic_sequences.fasta ; contigs_txt_rm /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/contigs_rm.txt ; tts_gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40_tts.gtf ; gene_gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40_gene.gtf ; contig_rm /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/contig_rm.tab ; gene /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/gene.tab ; stop_codon_gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40_stop_codon.gtf ; transcript /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/transcript.tab ; gene_start_gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40_gene_start.gtf ; gene_end_gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40_gene_end.gtf ; cds /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/cds.tab ; three_prime_utr_gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40_three_prime_utr.gtf ; log /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/log.txt ; exon /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/exon.tab ; organism /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/organism.tab ; contig /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/contig.tab ; tss_gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40_tss.gtf ; stop_codon /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/stop_codon.tab ; start_codon_gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40_start_codon.gtf ; five_prime_utr_gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40_five_prime_utr.gtf ; transcript_gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40_transcript.gtf ; fasta_lengths /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40.dna.toplevel_lengths.tab ; start_codon /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/start_codon.tab ; contigs_txt /var/www/html/rsat/public_html/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/contigs.txt ; fasta_pep_lengths /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40.pep.all_lengths.tab ; fasta_rm_lengths /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40.dna_rm.genome_lengths.tab ; exon_gtf /var/www/html/rsat/data/genomes/Setaria_italica.Setaria_italica_v2.0.40/genome/Setaria_italica.Setaria_italica_v2.0.40_exon.gtf ; Parsed rows per feature type ; cds 192057 ; exon 192116 ; five_prime_utr 19220 ; gene 35831 ; start_codon 38830 ; stop_codon 22415 ; three_prime_utr 24568 ; transcript 41023 ; Parsed rows per contig ; Contig Total cds exon five_prime_utr gene start stop three_prime_utr transcript ; I 65880 22640 22644 2263 4001 4385 2441 2890 4616 ; II 71447 24206 24217 2342 4594 4927 2871 3065 5225 ; III 67214 22692 22696 2397 4252 4644 2642 3014 4877 ; IV 48170 16288 16296 1647 3048 3316 1991 2077 3507 ; IX 100904 34697 34706 3465 6076 6683 3725 4482 7070 ; KQ475381 188 59 59 8 13 15 9 10 15 ; KQ475382 559 176 177 20 44 45 23 28 46 ; KQ475383 538 116 116 21 74 63 52 22 74 ; KQ475384 159 44 44 9 14 14 12 7 15 ; KQ475385 589 149 149 14 73 61 54 16 73 ; KQ475386 12 3 3 1 1 1 1 1 1 ; KQ475388 19 6 6 0 2 2 1 0 2 ; KQ475389 17 4 4 2 1 2 2 0 2 ; KQ475390 8 2 2 0 1 1 1 0 1 ; KQ475392 34 10 10 0 4 4 2 0 4 ; KQ475394 32 6 6 0 5 5 5 0 5 ; KQ475395 10 2 2 1 1 1 1 1 1 ; KQ475397 86 24 24 5 7 8 4 6 8 ; KQ475399 16 3 3 2 2 2 0 2 2 ; KQ475401 20 6 6 0 2 2 1 1 2 ; KQ475405 7 1 1 1 1 1 0 1 1 ; KQ475408 6 1 1 0 1 1 1 0 1 ; KQ475409 24 4 4 3 3 3 1 3 3 ; KQ475410 14 3 3 0 2 2 2 0 2 ; KQ475411 32 14 14 0 1 1 1 0 1 ; KQ475414 43 11 11 2 5 5 2 2 5 ; KQ475416 7 1 1 1 1 1 0 1 1 ; KQ475421 8 2 2 0 1 1 1 0 1 ; KQ475422 17 5 5 0 2 1 2 0 2 ; KQ475423 42 14 14 2 3 3 1 2 3 ; KQ475425 9 2 2 1 1 1 0 1 1 ; KQ475433 5 1 1 0 1 1 0 0 1 ; KQ475435 6 1 1 0 1 1 1 0 1 ; KQ475444 14 4 4 0 2 0 2 0 2 ; KQ475451 8 2 2 0 1 1 0 1 1 ; KQ475453 19 6 6 0 2 1 2 0 2 ; KQ475458 19 3 3 1 3 3 2 1 3 ; KQ475459 19 6 6 0 1 2 0 2 2 ; KQ475473 8 2 2 0 1 1 1 0 1 ; KQ475476 7 1 1 1 1 1 0 1 1 ; KQ475489 5 1 1 0 1 1 0 0 1 ; KQ475491 5 1 1 0 1 1 0 0 1 ; KQ475516 10 3 3 0 1 1 1 0 1 ; KQ475525 18 7 7 0 1 1 1 0 1 ; KQ475527 18 7 7 0 1 1 1 0 1 ; KQ475532 7 2 2 0 1 0 1 0 1 ; KQ475533 7 2 2 0 1 1 0 0 1 ; KQ475546 8 1 1 1 1 1 1 1 1 ; KQ475547 10 2 2 1 1 1 1 1 1 ; KQ475551 19 8 8 0 1 1 0 0 1 ; KQ475555 9 3 3 0 1 0 1 0 1 ; KQ475570 10 3 3 0 1 1 0 1 1 ; KQ475572 6 1 1 0 1 1 1 0 1 ; KQ475573 20 5 5 1 2 2 1 2 2 ; KQ475574 8 2 2 0 1 1 1 0 1 ; KQ475578 6 1 1 0 1 1 1 0 1 ; KQ475585 6 1 1 0 1 1 1 0 1 ; KQ475586 15 2 2 2 2 2 1 2 2 ; KQ475590 13 2 2 1 2 2 1 1 2 ; KQ475592 11 4 4 0 1 1 0 0 1 ; KQ475599 10 2 2 1 1 1 1 1 1 ; KQ475601 9 2 2 1 1 1 0 1 1 ; KQ475615 5 1 1 0 1 1 0 0 1 ; KQ475619 32 13 13 1 1 1 1 1 1 ; KQ475625 7 2 2 0 1 0 1 0 1 ; KQ475626 6 1 1 0 1 1 1 0 1 ; KQ475642 6 1 1 0 1 1 1 0 1 ; KQ475666 8 2 2 0 1 1 1 0 1 ; KQ475667 9 3 3 0 1 0 1 0 1 ; KQ475669 5 1 1 0 1 0 1 0 1 ; KQ475687 12 3 3 1 1 1 1 1 1 ; KQ475698 7 1 1 1 1 1 0 1 1 ; V 81267 27954 27963 2765 4897 5435 3045 3530 5678 ; VI 39096 13049 13054 1315 2606 2788 1662 1672 2950 ; VII 55090 18810 18815 1775 3466 3741 2196 2326 3961 ; VIII 34064 10937 10940 1145 2578 2624 1632 1390 2818 ; Host name baobab.eead.csic.es ; Job started 2018-09-24.090826 ; Job done 2018-09-24.140519 ; Seconds 69.89 ; user 69.9 ; system 33.08 ; cuser 17303.28 ; csystem 427.5