; 2021-02-18.120342 peak-motifs -i W7/regulonW7.rm.fna -ctrl Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna -motif_db footDB transfac $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -prefix peaks -outdir W7/regulonW7.rm.fna.peaks-rm -title W7/regulonW7.rm.fna -markov 2 -origin end -disco oligos,dyads,positions,local_words -nmotifs 5 -minol 5 -maxol 7 -scan_markov 1 -noov -img_format png -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_db,synthesis,small_summary,clean_seq ; 2021-02-18.120342 rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg W7/regulonW7.rm.fna.peaks-rm/images_html ; 2021-02-18.120342 $RSAT/perl-scripts/convert-seq -i W7/regulonW7.rm.fna -from fasta -to fasta -mask non-dna -o W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test.fasta ; 2021-02-18.120342 $RSAT/perl-scripts/purge-sequence -dna -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -ml 40 -mis 3 -o W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta ; 2021-02-18.120343 $RSAT/perl-scripts/sequence-lengths -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -o W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen.tab -ci 20 -o W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.tab ; 2021-02-18.120343 $RSAT/perl-scripts/XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; W7/regulonW7.rm.fna' -xsize 700 -xcol 3 -xleg1 'Peak length' -ysize 250 -ycol 4 -yleg1 'Number of peaks' -xmin 0 -ymin 0 -xgstep2 20 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.tab -o W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.png ; 2021-02-18.120344 time ($RSAT/bin/count-words -v 1 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -l 1 -1str > W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab_time.txt ; 2021-02-18.120344 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png ; 2021-02-18.120344 time ($RSAT/bin/count-words -v 1 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -l 2 -1str > W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab_time.txt ; 2021-02-18.120344 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_2nt.png ; 2021-02-18.120345 time ($RSAT/perl-scripts/position-analysis -v 1 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -format fasta -sort -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 1 -ci 20 -img_format png -title 'W7/regulonW7.rm.fna' -origin end -offset 0 -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab_time.txt ; 2021-02-18.120349 grep -v ";" W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-5 -xgstep2 20 -vline '#666666' 0 -xsize 700 -ysize 250 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/1nt-1str_colors.tab -title 'Nucleotide composition profiles; test sequence; W7/regulonW7.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250 -ymin 0 -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.png ; 2021-02-18.120349 time ($RSAT/perl-scripts/position-analysis -v 1 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -format fasta -sort -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title 'W7/regulonW7.rm.fna' -origin end -offset 0 -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab_time.txt ; 2021-02-18.120356 grep -v ";" W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-17 -xgstep2 20 -vline '#666666' 0 -xsize 700 -ysize 250 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/2nt-1str_colors.tab -title 'Dinucleotide composition profiles; test sequence; W7/regulonW7.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250 -ymin 0 -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.png ; 2021-02-18.120356 $RSAT/perl-scripts/convert-seq -i Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna -from fasta -to fasta -mask non-dna -o W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl.fasta ; 2021-02-18.120401 $RSAT/perl-scripts/purge-sequence -dna -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl.fasta -ml 40 -mis 3 -o W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta ; 2021-02-18.121728 $RSAT/perl-scripts/sequence-lengths -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -o W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen.tab -ci 20 -o W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.tab ; 2021-02-18.121731 $RSAT/perl-scripts/XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; W7/regulonW7.rm.fna' -xsize 700 -xcol 3 -xleg1 'Peak length' -ysize 250 -ycol 4 -yleg1 'Number of peaks' -xmin 0 -ymin 0 -xgstep2 20 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.tab -o W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.png ; 2021-02-18.121731 time ($RSAT/bin/count-words -v 1 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -l 1 -1str > W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab_time.txt ; 2021-02-18.121732 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png ; 2021-02-18.121732 time ($RSAT/bin/count-words -v 1 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -l 2 -1str > W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab_time.txt ; 2021-02-18.121733 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png ; 2021-02-18.121734 time ($RSAT/perl-scripts/position-analysis -v 1 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -sort -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 1 -ci 20 -img_format png -title 'W7/regulonW7.rm.fna' -origin end -offset 0 -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab_time.txt ; 2021-02-18.122308 grep -v ";" W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-5 -xgstep2 20 -vline '#666666' 0 -xsize 700 -ysize 250 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/1nt-1str_colors.tab -title 'Nucleotide composition profiles; ctrl sequence; W7/regulonW7.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250 -ymin 0 -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.png ; 2021-02-18.122308 time ($RSAT/perl-scripts/position-analysis -v 1 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -sort -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title 'W7/regulonW7.rm.fna' -origin end -offset 0 -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab_time.txt ; 2021-02-18.122937 grep -v ";" W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-17 -xgstep2 20 -vline '#666666' 0 -xsize 700 -ysize 250 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/2nt-1str_colors.tab -title 'Dinucleotide composition profiles; ctrl sequence; W7/regulonW7.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250 -ymin 0 -o W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.png ; 2021-02-18.122937 $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 5 -o W7/regulonW7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_5nt-2str-noov.tab ; 2021-02-18.122942 $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 6 -o W7/regulonW7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab ; 2021-02-18.122948 $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 7 -o W7/regulonW7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab ; 2021-02-18.122956 $RSAT/perl-scripts/dyad-analysis -v 1 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -quick -format fasta -return occ,freq -2str -noov -seqtype dna -l 3 -sp 0-20 -o W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab ; 2021-02-18.123114 time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 5 -expfreq W7/regulonW7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_5nt-2str-noov.tab -pseudo 0.01 -o W7/regulonW7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos-2str-noov_5nt_test_vs_ctrl.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos-2str-noov_5nt_test_vs_ctrl.tab_time.txt ; 2021-02-18.123115 time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 6 -expfreq W7/regulonW7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab -pseudo 0.01 -o W7/regulonW7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab_time.txt ; 2021-02-18.123116 time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 7 -expfreq W7/regulonW7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab -pseudo 0.01 -o W7/regulonW7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab_time.txt ; 2021-02-18.123119 cat W7/regulonW7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos-2str-noov_5nt_test_vs_ctrl.tab W7/regulonW7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab W7/regulonW7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab> W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2.tab ; 2021-02-18.123119 time ($RSAT/perl-scripts/matrix-from-patterns -v 1 -sites -seq W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -pl W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2.tab -bgfile W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_5-7nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm) >& W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_time.txt ; 2021-02-18.123131 time ($RSAT/perl-scripts/dyad-analysis -v 1 -i W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -quick -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,ratio,zscore,rank -2str -noov -seqtype dna -l 3 -sp 0-20 -expfreq W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab -pseudo 0.01 | perl -pe 's/n\{0\}//g' >W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab_time.txt ; 2021-02-18.123148 time ($RSAT/perl-scripts/matrix-from-patterns -v 1 -sites -seq W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -pl W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -bgfile W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix dyads_test_vs_ctrl -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm) >& W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_time.txt ; 2021-02-18.123224 rm -f W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf; cat W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf >> W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf; cat W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf >> W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf ; 2021-02-18.123224 $RSAT/perl-scripts/convert-matrix -v 0 -i W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1.tf -from transfac -to tab -return counts -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1.tab ; 2021-02-18.123225 $RSAT/perl-scripts/convert-matrix -v 0 -i W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/peaks_oligos_5-7nt_m2.tf -from transfac -to tab -return counts -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/peaks_oligos_5-7nt_m2.tab ; 2021-02-18.123225 $RSAT/perl-scripts/convert-matrix -v 0 -i W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/peaks_oligos_5-7nt_m3.tf -from transfac -to tab -return counts -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/peaks_oligos_5-7nt_m3.tab ; 2021-02-18.123225 $RSAT/perl-scripts/convert-matrix -v 0 -i W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/peaks_oligos_5-7nt_m4.tf -from transfac -to tab -return counts -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/peaks_oligos_5-7nt_m4.tab ; 2021-02-18.123225 $RSAT/perl-scripts/convert-matrix -v 0 -i W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5.tf -from transfac -to tab -return counts -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5.tab ; 2021-02-18.123226 $RSAT/perl-scripts/convert-matrix -v 0 -i W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tf -from transfac -to tab -return counts -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tab ; 2021-02-18.123226 $RSAT/perl-scripts/convert-matrix -v 0 -i W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tf -from transfac -to tab -return counts -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tab ; 2021-02-18.123226 $RSAT/perl-scripts/convert-matrix -v 0 -i W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tf -from transfac -to tab -return counts -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tab ; 2021-02-18.123226 $RSAT/perl-scripts/convert-matrix -v 0 -i W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tf -from transfac -to tab -return counts -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tab ; 2021-02-18.123227 $RSAT/perl-scripts/convert-matrix -v 0 -i W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tf -from transfac -to tab -return counts -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tab ; 2021-02-18.123227 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1_vs_db_footDB ; 2021-02-18.123231 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/peaks_oligos_5-7nt_m2.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/peaks_oligos_5-7nt_m2_vs_db_footDB ; 2021-02-18.123236 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/peaks_oligos_5-7nt_m3.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/peaks_oligos_5-7nt_m3_vs_db_footDB ; 2021-02-18.123241 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/peaks_oligos_5-7nt_m4.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/peaks_oligos_5-7nt_m4_vs_db_footDB ; 2021-02-18.123245 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_vs_db_footDB ; 2021-02-18.123250 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footDB ; 2021-02-18.123255 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footDB ; 2021-02-18.123301 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_db_footDB ; 2021-02-18.123306 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_db_footDB ; 2021-02-18.123311 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_vs_db_footDB ; 2021-02-18.123316 time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab) >& W7/regulonW7.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab_time.txt ; 2021-02-18.123325 $RSAT/perl-scripts/convert-graph -i W7/regulonW7.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o W7/regulonW7.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.gml ; peak-motifs -i W7/regulonW7.rm.fna -ctrl Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna -motif_db footDB transfac $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -prefix peaks -outdir W7/regulonW7.rm.fna.peaks-rm -title W7/regulonW7.rm.fna -markov 2 -origin end -disco oligos,dyads,positions,local_words -nmotifs 5 -minol 5 -maxol 7 -scan_markov 1 -noov -img_format png -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_db,synthesis,small_summary,clean_seq ; Program version 1.256 ; Parameter values ; seq_format fasta ; img_format png ; ref_motifs_format transfac ; purge_match_length 40 ; purge_mismatches 3 ; origin end ; offset 0 ; profiles_ci 20 ; profiles_max_graphs 20 ; profiles_strand -1str ; composition_oligo_lengths 1,2 ; profiles_noov -ovlp ; strand -2str ; disco_noov -noov ; oligo_min_len 5 ; oligo_max_len 7 ; patterns_max_rank 100 ; min_ratio 1 ; min_zscore 6 ; min_sig 0 ; oligo_min_mkv 2 ; oligo_max_mkv 2 ; under_represented 0 ; positions_max_graphs 20 ; asmb_toppat 100 ; max_asmb_width 20 ; matrix_nmotifs 5 ; Input files ; ctrl_seq Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna ; motif_db_footDB /var/www/html/rsat/_footprintDB/footprintDB.transfac.plants.motif.tf ; test_seq W7/regulonW7.rm.fna ; Directories ; output W7/regulonW7.rm.fna.peaks-rm/ ; oligos_5-7nt_m1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/ ; oligos_5-7nt_m2 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/ ; oligos_5-7nt_m3 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/ ; oligos_5-7nt_m4 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/ ; oligos_5-7nt_m5 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/ ; dyads_test_vs_ctrl_m1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/ ; dyads_test_vs_ctrl_m2 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/ ; dyads_test_vs_ctrl_m3 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/ ; dyads_test_vs_ctrl_m4 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/ ; dyads_test_vs_ctrl_m5 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/ ; Output files ; 1nt_ctrl_freq W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab ; 1nt_ctrl_heatmap W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png ; 1nt_ctrl_inclusive W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt ; 1nt_ctrl_profiles W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab ; 1nt_ctrl_profiles_graph W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.png ; 1nt_ctrl_profiles_index W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20_graph_index.html ; 1nt_ctrl_transitions W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab ; 1nt_test_freq W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab ; 1nt_test_heatmap W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png ; 1nt_test_inclusive W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_1nt.txt ; 1nt_test_profiles W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab ; 1nt_test_profiles_graph W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.png ; 1nt_test_profiles_index W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20_graph_index.html ; 1nt_test_transitions W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab ; 2nt_ctrl_freq W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab ; 2nt_ctrl_heatmap W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png ; 2nt_ctrl_inclusive W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_2nt.txt ; 2nt_ctrl_profiles W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab ; 2nt_ctrl_profiles_graph W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.png ; 2nt_ctrl_profiles_index W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20_graph_index.html ; 2nt_ctrl_transitions W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab ; 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oligos_5-7nt_m5_logo_rc W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_logo_rc.png ; oligos_5-7nt_m5_pssm_enrichment W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_scan_mkv1_enrichment.tab ; oligos_5-7nt_m5_pssm_enrichment_png W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_scan_mkv1_enrichment.png ; oligos_5-7nt_m5_pssm_site_distrib W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_site_distrib.tab ; oligos_5-7nt_m5_pssm_site_distrib_graph W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_site_distrib.png ; oligos_5-7nt_m5_pssm_sites W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_sites.tab ; oligos_5-7nt_m5_pssm_sites_per_peak W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_sites_per_peak.tab ; oligos_5-7nt_m5_pssm_sites_per_peak_graph W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_sites_per_peak.png ; oligos_5-7nt_m5_tab W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5.tab ; oligos_5-7nt_m5_tf W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5.tf ; oligos_5-7nt_m5_vs_db_footDB W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_vs_db_footDB.tab ; oligos_5-7nt_m5_vs_db_footDB_html W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_vs_db_footDB.html ; oligos_5-7nt_m5_vs_ref W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_vs_ref.tab ; oligos_5-7nt_m5_vs_ref_html W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_vs_ref.html ; oligos_5-7nt_pssm_counts W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.txt ; oligos_5-7nt_pssm_logo1 W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m1.png ; oligos_5-7nt_pssm_logo2 W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m2.png ; oligos_5-7nt_pssm_logo3 W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m3.png ; oligos_5-7nt_pssm_logo4 W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m4.png ; oligos_5-7nt_pssm_logo5 W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m5.png ; oligos_5-7nt_pssm_logo_rc1 W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m1_rc.png ; oligos_5-7nt_pssm_logo_rc2 W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m2_rc.png ; oligos_5-7nt_pssm_logo_rc3 W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m3_rc.png ; oligos_5-7nt_pssm_logo_rc4 W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m4_rc.png ; oligos_5-7nt_pssm_logo_rc5 W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m5_rc.png ; oligos_5-7nt_pssm_sig W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices.tf ; oligos_5-7nt_pssm_tf W7/regulonW7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf ; oligos_5nt_test_vs_ctrl W7/regulonW7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos-2str-noov_5nt_test_vs_ctrl.tab ; oligos_5nt_test_vs_ctrl_bg_file W7/regulonW7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_5nt-2str-noov.tab ; oligos_6nt_test_vs_ctrl W7/regulonW7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab ; oligos_6nt_test_vs_ctrl_bg_file W7/regulonW7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab ; oligos_7nt_test_vs_ctrl W7/regulonW7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab ; oligos_7nt_test_vs_ctrl_bg_file W7/regulonW7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab ; small_summary W7/regulonW7.rm.fna.peaks-rm/peaks_small_summary.html ; small_summary_txt W7/regulonW7.rm.fna.peaks-rm/reports/peaks_small_summary.txt ; synthesis W7/regulonW7.rm.fna.peaks-rm/peaks_synthesis.html ; test_converted W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test.fasta ; test_purged W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta ; test_seqlen W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen.tab ; test_seqlen_distrib W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.tab ; test_seqlen_distrib_graph W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.png ; timelog W7/regulonW7.rm.fna.peaks-rm/reports/peaks_timelog.txt ; timelog_html W7/regulonW7.rm.fna.peaks-rm/reports/peaks_timelog.html ; timetable W7/regulonW7.rm.fna.peaks-rm/reports/peaks_timetable.txt ; 2021-02-18.123425 rm -f W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta ; 2021-02-18.123425 rm -f W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta ; 2021-02-18.123425 rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg W7/regulonW7.rm.fna.peaks-rm/images_html ; peak-motifs -i W7/regulonW7.rm.fna -ctrl Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna -motif_db footDB transfac $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -prefix peaks -outdir W7/regulonW7.rm.fna.peaks-rm -title W7/regulonW7.rm.fna -markov 2 -origin end -disco oligos,dyads,positions,local_words -nmotifs 5 -minol 5 -maxol 7 -scan_markov 1 -noov -img_format png -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_db,synthesis,small_summary,clean_seq ; Program version 1.256 ; Parameter values ; seq_format fasta ; img_format png ; ref_motifs_format transfac ; purge_match_length 40 ; purge_mismatches 3 ; origin end ; offset 0 ; profiles_ci 20 ; profiles_max_graphs 20 ; profiles_strand -1str ; composition_oligo_lengths 1,2 ; profiles_noov -ovlp ; strand -2str ; disco_noov -noov ; oligo_min_len 5 ; oligo_max_len 7 ; patterns_max_rank 100 ; min_ratio 1 ; min_zscore 6 ; min_sig 0 ; oligo_min_mkv 2 ; oligo_max_mkv 2 ; under_represented 0 ; positions_max_graphs 20 ; asmb_toppat 100 ; max_asmb_width 20 ; matrix_nmotifs 5 ; Input files ; ctrl_seq Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna ; motif_db_footDB /var/www/html/rsat/_footprintDB/footprintDB.transfac.plants.motif.tf ; test_seq W7/regulonW7.rm.fna ; Directories ; output W7/regulonW7.rm.fna.peaks-rm/ ; oligos_5-7nt_m1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/ ; oligos_5-7nt_m2 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/ ; oligos_5-7nt_m3 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/ ; oligos_5-7nt_m4 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/ ; oligos_5-7nt_m5 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/ ; dyads_test_vs_ctrl_m1 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/ ; dyads_test_vs_ctrl_m2 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/ ; dyads_test_vs_ctrl_m3 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/ ; dyads_test_vs_ctrl_m4 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/ ; dyads_test_vs_ctrl_m5 W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/ ; Output files ; 1nt_ctrl_freq W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab ; 1nt_ctrl_heatmap W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png ; 1nt_ctrl_inclusive W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt ; 1nt_ctrl_profiles W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab ; 1nt_ctrl_profiles_graph W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.png ; 1nt_ctrl_profiles_index W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20_graph_index.html ; 1nt_ctrl_transitions W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab ; 1nt_test_freq W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab ; 1nt_test_heatmap W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png ; 1nt_test_inclusive W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_1nt.txt ; 1nt_test_profiles W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab ; 1nt_test_profiles_graph W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.png ; 1nt_test_profiles_index W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20_graph_index.html ; 1nt_test_transitions W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab ; 2nt_ctrl_freq W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab ; 2nt_ctrl_heatmap W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png ; 2nt_ctrl_inclusive W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_2nt.txt ; 2nt_ctrl_profiles W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab ; 2nt_ctrl_profiles_graph W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.png ; 2nt_ctrl_profiles_index W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20_graph_index.html ; 2nt_ctrl_transitions W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab ; 2nt_test_freq W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab ; 2nt_test_heatmap W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_2nt.png ; 2nt_test_inclusive W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt ; 2nt_test_profiles W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab ; 2nt_test_profiles_graph W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.png ; 2nt_test_profiles_index W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20_graph_index.html ; 2nt_test_transitions W7/regulonW7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab ; archive W7/regulonW7.rm.fna.peaks-rm/peaks_archive.zip ; ctrl_converted W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl.fasta ; ctrl_purged W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta ; ctrl_seqlen W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen.tab ; ctrl_seqlen_distrib W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.tab ; ctrl_seqlen_distrib_graph W7/regulonW7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.png ; dyads_test_vs_ctrl W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab ; dyads_test_vs_ctrl_2pssm W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt ; dyads_test_vs_ctrl_asmb W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb ; dyads_test_vs_ctrl_bg_file W7/regulonW7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab ; dyads_test_vs_ctrl_m1_logo W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_logo.png ; dyads_test_vs_ctrl_m1_logo_rc W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_logo_rc.png ; dyads_test_vs_ctrl_m1_pssm_enrichment W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_scan_mkv1_enrichment.tab ; dyads_test_vs_ctrl_m1_pssm_enrichment_png W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_scan_mkv1_enrichment.png ; dyads_test_vs_ctrl_m1_pssm_site_distrib W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_site_distrib.tab ; dyads_test_vs_ctrl_m1_pssm_site_distrib_graph W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_site_distrib.png ; dyads_test_vs_ctrl_m1_pssm_sites W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites.tab ; dyads_test_vs_ctrl_m1_pssm_sites_per_peak W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites_per_peak.tab ; dyads_test_vs_ctrl_m1_pssm_sites_per_peak_graph W7/regulonW7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites_per_peak.png ; 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