; parse-gtf -v 2 -i $RSAT/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI.gtf -fasta $RSAT/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI.pep.all.fa -org_name Brachypodium_stacei.316.v1.1.JGI -task all -taxid 1071399 -gtf_source JGI -o $RSAT/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome ; Program version 1.48 ; Input files ; fasta_rm /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI.dna_rm.genome.fa ; gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI.gtf ; fasta /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI.dna.toplevel.fa ; fasta_pep /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI.pep.all.fa ; Output files ; peptidic_sequences /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/peptidic_sequences.fasta ; contigs_txt_rm /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/contigs_rm.txt ; tts_gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI_tts.gtf ; gene_gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI_gene.gtf ; contig_rm /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/contig_rm.tab ; gene /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/gene.tab ; stop_codon_gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI_stop_codon.gtf ; transcript /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/transcript.tab ; gene_start_gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI_gene_start.gtf ; gene_end_gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI_gene_end.gtf ; cds /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/cds.tab ; three_prime_utr_gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI_three_prime_utr.gtf ; log /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/log.txt ; exon /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/exon.tab ; organism /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/organism.tab ; contig /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/contig.tab ; tss_gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI_tss.gtf ; stop_codon /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/stop_codon.tab ; start_codon_gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI_start_codon.gtf ; five_prime_utr_gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI_five_prime_utr.gtf ; transcript_gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI_transcript.gtf ; fasta_lengths /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI.dna.toplevel_lengths.tab ; start_codon /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/start_codon.tab ; contigs_txt /var/www/html/rsat/public_html/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/contigs.txt ; fasta_pep_lengths /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI.pep.all_lengths.tab ; fasta_rm_lengths /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI.dna_rm.genome_lengths.tab ; exon_gtf /var/www/html/rsat/data/genomes/Brachypodium_stacei.316.v1.1.JGI/genome/Brachypodium_stacei.316.v1.1.JGI_exon.gtf ; Parsed rows per feature type ; 3 ; cds 191895 ; five_prime_utr 35533 ; gene 29898 ; mrna 36357 ; three_prime_utr 34591 ; Parsed rows per contig ; Contig Total cds five_prime_utr gene mrna three_prime_utr ; ##annot-version v1.1 1 1 0 0 0 0 0 ; ##gff-version 3 1 1 0 0 0 0 0 ; ##species Brachypodium stacei 1 1 0 0 0 0 0 ; Chr01 47812 0 28443 5113 4150 5123 4983 ; Chr02 43742 0 25514 4835 3958 4798 4637 ; Chr03 34407 0 20070 3714 3131 3832 3660 ; Chr04 39856 0 23742 4282 3438 4190 4204 ; Chr05 31158 0 17846 3401 3021 3606 3284 ; Chr06 26035 0 15104 2716 2479 2975 2761 ; Chr07 27215 0 16044 2906 2468 3000 2797 ; Chr08 26596 0 15303 2977 2505 3004 2807 ; Chr09 30283 0 17760 3240 2718 3341 3224 ; Chr10 21011 0 12006 2319 2010 2463 2213 ; scaffold_106 7 0 3 1 1 1 1 ; scaffold_108 5 0 1 2 1 1 0 ; scaffold_13 4 0 2 0 1 1 0 ; scaffold_19 19 0 8 4 2 3 2 ; scaffold_21 25 0 13 1 3 4 4 ; scaffold_30 20 0 10 5 1 2 2 ; scaffold_31 12 0 3 4 1 1 3 ; scaffold_34 5 0 1 1 1 1 1 ; scaffold_41 6 0 2 1 1 1 1 ; scaffold_48 6 0 4 0 1 1 0 ; scaffold_51 12 0 5 2 1 2 2 ; scaffold_66 4 0 2 0 1 1 0 ; scaffold_71 3 0 1 0 1 1 0 ; scaffold_82 11 0 2 4 1 2 2 ; scaffold_89 7 0 2 2 1 1 1 ; scaffold_90 7 0 2 2 1 1 1 ; scaffold_91 6 0 2 1 1 1 1 ; Host name baobab.eead.csic.es ; Job started 2020-07-03.115405 ; Job done 2020-07-03.151016 ; Seconds 35.19 ; user 35.19 ; system 1.4 ; cuser 11661.84 ; csystem 117.3