; parse-gtf -v 2 -i $RSAT/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.gtf -fasta $RSAT/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.pep.all.fa -org_name Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq -task all -taxid 3702 -gtf_source NCBIRefseq -o $RSAT/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome ; Program version 1.48 ; Input files ; fasta_rm /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.dna_rm.genome.fa ; gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.gtf ; fasta /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.dna.toplevel.fa ; fasta_pep /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.pep.all.fa ; Output files ; peptidic_sequences /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/peptidic_sequences.fasta ; contigs_txt_rm /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/contigs_rm.txt ; tts_gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq_tts.gtf ; gene_gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq_gene.gtf ; contig_rm /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/contig_rm.tab ; gene /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/gene.tab ; stop_codon_gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq_stop_codon.gtf ; transcript /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/transcript.tab ; gene_start_gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq_gene_start.gtf ; gene_end_gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq_gene_end.gtf ; cds /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/cds.tab ; three_prime_utr_gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq_three_prime_utr.gtf ; log /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/log.txt ; exon /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/exon.tab ; organism /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/organism.tab ; contig /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/contig.tab ; tss_gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq_tss.gtf ; stop_codon /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/stop_codon.tab ; start_codon_gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq_start_codon.gtf ; five_prime_utr_gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq_five_prime_utr.gtf ; transcript_gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq_transcript.gtf ; fasta_lengths /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.dna.toplevel_lengths.tab ; start_codon /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/start_codon.tab ; contigs_txt /var/www/html/rsat/public_html/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/contigs.txt ; fasta_pep_lengths /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.pep.all_lengths.tab ; fasta_rm_lengths /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.dna_rm.genome_lengths.tab ; exon_gtf /var/www/html/rsat/data/genomes/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq/genome/Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq_exon.gtf ; Parsed rows per feature type ; 16 ; antisense_rna 92 ; cds 286353 ; exon 324438 ; gene 38161 ; intron 22 ; lnc_rna 3878 ; mirna 427 ; mrna 52060 ; ncrna 286 ; primary_transcript 325 ; promoter 14 ; region 7 ; repeat_region 3 ; repeat_unit 3 ; rrna 14 ; sequence_feature 566 ; snorna 287 ; snrna 82 ; transcript 1826 ; trna 683 ; Parsed rows per contig ; Contig Total antisense_rna cds exon gene intron lnc_rna mirna mrna ncrna primary_transcript promoter region repeat_region repeat_unit rrna sequence_feature snorna snrna transcript trna ; ### 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ; ##gff-version 3 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ; ##sequence-region NC_000932.1 1 154478 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ; ##sequence-region NC_001284.2 1 366924 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ; ##sequence-region NC_003070.9 1 30427671 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ; ##sequence-region NC_003071.7 1 19698289 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ; ##sequence-region NC_003074.8 1 23459830 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ; ##sequence-region NC_003075.7 1 18585056 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ; ##sequence-region NC_003076.8 1 26975502 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ; ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3702 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ; NC_000932.1 332 0 0 104 52 131 0 0 0 0 0 0 0 1 0 0 7 0 0 0 0 37 ; NC_001284.2 850 0 0 140 56 132 22 0 0 0 0 0 14 1 3 3 3 455 0 0 0 21 ; NC_003070.9 190232 0 20 77649 87306 9701 0 1098 115 13337 86 89 0 1 0 0 0 31 89 22 450 238 ; NC_003071.7 110571 0 21 43844 50533 6312 0 683 74 8431 55 55 0 1 0 0 2 12 46 4 403 95 ; NC_003074.8 137145 0 25 54878 62765 7624 0 763 67 10353 56 50 0 1 0 0 2 19 47 19 384 92 ; NC_003075.7 109376 0 14 44130 50105 5842 0 559 69 8137 49 55 0 1 0 0 0 12 44 10 272 77 ; NC_003076.8 161021 0 12 65608 73621 8419 0 775 102 11802 40 76 0 1 0 0 0 37 61 27 317 123 ; Host name baobab.eead.csic.es ; Job started 2017-12-28.153333 ; Job done 2017-12-28.175350 ; Seconds 56.57 ; user 56.57 ; system 4.33 ; cuser 6320.57 ; csystem 159.83