; parse-gtf -v 2 -i $RSAT/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34.gtf -fasta $RSAT/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34.pep.all.fa -org_name Toxoplasma_gondii.ToxoDB-7.1.34 -task all -taxid 508771 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome ; Program version 1.48 ; Input files ; fasta /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34.dna.toplevel.fa ; gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34.gtf ; fasta_rm /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34.dna_rm.genome.fa ; fasta_pep /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34.pep.all.fa ; Output files ; peptidic_sequences /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/peptidic_sequences.fasta ; fasta_rm_lengths /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34.dna_rm.genome_lengths.tab ; tss_gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34_tss.gtf ; gene_end_gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34_gene_end.gtf ; exon /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/exon.tab ; log /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/log.txt ; gene_gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34_gene.gtf ; transcript_gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34_transcript.gtf ; gene_start_gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34_gene_start.gtf ; five_prime_utr_gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34_five_prime_utr.gtf ; fasta_lengths /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34.dna.toplevel_lengths.tab ; three_prime_utr_gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34_three_prime_utr.gtf ; start_codon /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/start_codon.tab ; cds /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/cds.tab ; start_codon_gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34_start_codon.gtf ; stop_codon /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/stop_codon.tab ; contig /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/contig.tab ; contigs_txt_rm /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/contigs_rm.txt ; contigs_txt /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/contigs.txt ; gene /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/gene.tab ; transcript /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/transcript.tab ; organism /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/organism.tab ; stop_codon_gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34_stop_codon.gtf ; exon_gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34_exon.gtf ; contig_rm /export/home1/rsat/rsat/public_html/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/contig_rm.tab ; fasta_pep_lengths /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34.pep.all_lengths.tab ; tts_gtf /export/home1/rsat/rsat/data/genomes/Toxoplasma_gondii.ToxoDB-7.1.34/genome/Toxoplasma_gondii.ToxoDB-7.1.34_tts.gtf ; Parsed rows per feature type ; cds 42485 ; exon 43175 ; five_prime_utr 3006 ; gene 8320 ; start_codon 7971 ; stop_codon 7976 ; three_prime_utr 3796 ; transcript 8320 ; Parsed rows per contig ; Contig Total cds exon five_prime_utr gene start stop three_prime_utr transcript ; ABPA01000206.1 7 1 1 1 1 1 1 0 1 ; ABPA01000213.1 55 19 20 2 3 3 3 2 3 ; ABPA01000240.1 12 3 3 1 1 1 1 1 1 ; ABPA01000251.1 58 5 12 4 12 5 5 3 12 ; ABPA01000275.1 8 2 2 0 1 1 1 0 1 ; ABPA01000277.1 16 3 3 1 2 2 2 1 2 ; ABPA01000280.1 24 7 7 1 2 2 2 1 2 ; ABPA01000289.1 35 3 8 1 8 3 3 1 8 ; ABPA01000309.1 6 1 1 0 1 1 1 0 1 ; ABPA01000322.1 11 3 3 1 1 1 1 0 1 ; ABPA01000335.1 6 1 1 1 1 0 1 0 1 ; ABPA01000336.1 6 1 1 0 1 1 1 0 1 ; ABPA01000351.1 6 1 1 0 1 1 1 0 1 ; ABPA01000365.1 6 1 1 0 1 1 1 0 1 ; ABPA01000369.1 6 1 1 0 1 1 1 0 1 ; ABPA01000379.1 10 2 2 1 1 1 1 1 1 ; ABPA01000380.1 6 1 1 0 1 1 1 0 1 ; ABPA01000382.1 6 1 1 0 1 1 1 0 1 ; ABPA01000398.1 6 1 1 0 1 1 1 0 1 ; ABPA01000421.1 14 3 3 0 2 2 2 0 2 ; ABPA01000426.1 15 6 6 0 1 0 1 0 1 ; ABPA01000436.1 3 0 1 0 1 0 0 0 1 ; ABPA01000440.1 14 5 5 0 1 1 1 0 1 ; ABPA01000442.1 18 7 7 1 1 0 1 0 1 ; ABPA01000445.1 15 6 6 0 1 1 0 0 1 ; ABPA01000446.1 12 4 4 1 1 0 1 0 1 ; ABPA01000462.1 14 5 5 0 1 1 0 1 1 ; ABPA01000463.1 6 1 1 0 1 1 1 0 1 ; ABPA01000465.1 16 7 7 0 1 0 0 0 1 ; ABPA01000478.1 6 1 1 0 1 1 1 0 1 ; ABPA01000509.1 12 5 5 0 1 0 0 0 1 ; ABPA01000517.1 9 3 3 0 1 0 1 0 1 ; ABPA01000528.1 5 1 1 0 1 1 0 0 1 ; ABPA01000541.1 12 4 4 1 1 0 1 0 1 ; ABPA01000556.1 6 1 1 1 1 0 1 0 1 ; ABPA01000567.1 10 3 3 1 1 0 1 0 1 ; ABPA01000581.1 6 1 1 0 1 1 1 0 1 ; ABPA01000588.1 6 1 1 1 1 0 1 0 1 ; ABPA01000590.1 12 5 5 0 1 0 0 0 1 ; ABPA01000591.1 11 4 4 0 1 0 0 1 1 ; ABPA01000610.1 3 0 1 0 1 0 0 0 1 ; ABPA01000613.1 12 5 5 0 1 0 0 0 1 ; ABPA01000629.1 3 0 1 0 1 0 0 0 1 ; ABPA01000634.1 13 5 5 1 1 0 0 0 1 ; ABPA01000640.1 5 1 1 0 1 1 0 0 1 ; ABPA01000645.1 10 3 3 0 1 1 1 0 1 ; ABPA01000655.1 5 1 1 0 1 0 1 0 1 ; ABPA01000685.1 6 1 1 0 1 1 1 0 1 ; ABPA01000692.1 7 2 2 0 1 1 0 0 1 ; ABPA01000697.1 3 0 1 0 1 0 0 0 1 ; DS984777.1 24 6 6 1 3 3 2 0 3 ; DS984783.1 6 1 1 0 1 1 1 0 1 ; DS984792.1 6 1 1 0 1 1 1 0 1 ; DS984796.1 6 1 1 0 1 1 1 0 1 ; DS984825.1 23 6 6 1 2 2 2 2 2 ; DS984844.1 6 1 1 0 1 1 1 0 1 ; DS984891.1 13 5 5 1 1 0 0 0 1 ; chrII 4547 1626 1648 96 270 259 258 120 270 ; chrIII 4479 1492 1508 95 317 307 307 136 317 ; chrIV 5092 1778 1799 99 321 315 315 144 321 ; chrIX 13021 4464 4527 303 852 824 825 374 852 ; chrIa 3677 1259 1277 85 240 231 231 114 240 ; chrIb 4049 1393 1430 108 260 240 240 118 260 ; chrV 5927 1965 2009 136 424 400 401 168 424 ; chrVI 7270 2468 2492 162 489 481 482 207 489 ; chrVIII 14294 4779 4884 387 969 923 923 460 969 ; chrVIIa 9049 3128 3166 208 572 555 556 292 572 ; chrVIIb 10771 3722 3766 232 686 670 669 340 686 ; chrX 14873 5015 5096 374 996 958 959 479 996 ; chrXI 12914 4340 4410 330 882 848 847 375 882 ; chrXII 14423 4887 4977 367 959 910 909 455 959 ; Host name rsat01 ; Job started 2017-02-27.072749 ; Job done 2017-02-27.073651 ; Seconds 7.23 ; user 7.23 ; system 0.34 ; cuser 524.13 ; csystem 15.86