; parse-gtf -v 2 -i $RSAT/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34.gtf -fasta $RSAT/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34.pep.all.fa -org_name Plasmodium_chabaudi.PCHAS01.34 -task all -taxid 31271 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome ; Program version 1.48 ; Input files ; fasta /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34.dna.toplevel.fa ; gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34.gtf ; fasta_pep /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34.pep.all.fa ; fasta_rm /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34.dna_rm.genome.fa ; Output files ; transcript_gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34_transcript.gtf ; contig /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/contig.tab ; gene /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/gene.tab ; stop_codon_gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34_stop_codon.gtf ; cds /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/cds.tab ; fasta_pep_lengths /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34.pep.all_lengths.tab ; gene_start_gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34_gene_start.gtf ; five_prime_utr_gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34_five_prime_utr.gtf ; tss_gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34_tss.gtf ; tts_gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34_tts.gtf ; exon_gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34_exon.gtf ; peptidic_sequences /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/peptidic_sequences.fasta ; start_codon /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/start_codon.tab ; fasta_rm_lengths /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34.dna_rm.genome_lengths.tab ; fasta_lengths /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34.dna.toplevel_lengths.tab ; contigs_txt_rm /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/contigs_rm.txt ; exon /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/exon.tab ; gene_end_gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34_gene_end.gtf ; three_prime_utr_gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34_three_prime_utr.gtf ; transcript /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/transcript.tab ; organism /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/organism.tab ; stop_codon /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/stop_codon.tab ; contig_rm /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/contig_rm.tab ; gene_gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34_gene.gtf ; log /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/log.txt ; start_codon_gtf /export/home1/rsat/rsat/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/Plasmodium_chabaudi.PCHAS01.34_start_codon.gtf ; contigs_txt /export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_chabaudi.PCHAS01.34/genome/contigs.txt ; Parsed rows per feature type ; cds 13926 ; exon 14098 ; gene 5295 ; start_codon 5164 ; stop_codon 5151 ; transcript 5295 ; Parsed rows per contig ; Contig Total cds exon gene start stop transcript ; 1 1536 458 458 155 155 155 155 ; 10 4043 1164 1170 430 425 424 430 ; 11 4307 1192 1203 483 474 472 483 ; 12 4226 1180 1183 467 465 464 467 ; 13 6931 2010 2044 727 713 710 727 ; 14 6232 1728 1742 696 685 685 696 ; 2 1317 379 381 140 139 138 140 ; 3 1719 495 497 183 181 180 183 ; 4 1999 574 583 213 209 207 213 ; 5 2445 709 712 258 254 254 258 ; 6 2393 698 703 250 246 246 250 ; 7 3284 996 1002 323 320 320 323 ; 8 3452 957 964 386 380 379 386 ; 9 3631 1023 1048 399 381 381 399 ; Mt 117 3 36 36 3 3 36 ; Pt 218 31 43 42 30 30 42 ; chab_bin_11_110540-114200 10 3 3 1 1 1 1 ; chab_bin_12_114201-116236 7 2 2 1 1 0 1 ; chab_bin_13_116237-119970 10 3 3 1 1 1 1 ; chab_bin_14_119971-133199 39 12 12 4 4 3 4 ; chab_bin_15_133200-145545 45 13 13 5 5 4 5 ; chab_bin_16_145546-208881 143 44 44 14 14 13 14 ; chab_bin_17_208882-222218 46 15 15 4 4 4 4 ; chab_bin_18_222219-247479 50 13 13 6 6 6 6 ; chab_bin_19_247480-261474 52 18 18 4 4 4 4 ; chab_bin_1_1-13354 46 15 15 4 4 4 4 ; chab_bin_20_261475-352890 192 56 56 20 20 20 20 ; chab_bin_21_352891-411999 123 36 36 13 12 13 13 ; chab_bin_22_412000-417365 17 5 5 2 1 2 2 ; chab_bin_23_417366-437237 66 21 21 6 6 6 6 ; chab_bin_4_17515-25521 36 12 12 3 3 3 3 ; chab_bin_5_25522-27699 7 2 2 1 0 1 1 ; chab_bin_6_27700-56706 88 28 28 8 8 8 8 ; chab_bin_8_58805-69438 20 6 6 2 2 2 2 ; chab_bin_9_69439-107949 82 25 25 8 8 8 8 ; Host name rsat01 ; Job started 2017-02-27.045807 ; Job done 2017-02-27.050408 ; Seconds 2.83 ; user 2.83 ; system 0.14 ; cuser 350.68 ; csystem 12.12