; 2021-02-16.163430 peak-motifs -i D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm -title D7/regulonD7.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 ; 2021-02-16.163430 rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg D7/regulonD7.rm.fna.peaks-rm/images_html ; 2021-02-16.163430 $RSAT/perl-scripts/convert-seq -i D7/regulonD7.rm.fna -from fasta -to fasta -mask non-dna -o D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test.fasta ; 2021-02-16.163430 $RSAT/perl-scripts/purge-sequence -dna -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -ml 40 -mis 3 -o D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta ; 2021-02-16.163431 $RSAT/perl-scripts/sequence-lengths -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -o D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen.tab -ci 20 -o D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.tab ; 2021-02-16.163431 $RSAT/perl-scripts/XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; D7/regulonD7.rm.fna' -xsize 700 -xcol 3 -xleg1 'Peak length' -ysize 250 -ycol 4 -yleg1 'Number of peaks' -xmin 0 -ymin 0 -xgstep2 20 -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.tab -o D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.png ; 2021-02-16.163431 time ($RSAT/bin/count-words -v 1 -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -l 1 -1str > D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab_time.txt ; 2021-02-16.163431 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png ; 2021-02-16.163432 time ($RSAT/bin/count-words -v 1 -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -l 2 -1str > D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab_time.txt ; 2021-02-16.163432 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_2nt.png ; 2021-02-16.163432 time ($RSAT/perl-scripts/position-analysis -v 1 -i D7/regulonD7.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 'D7/regulonD7.rm.fna' -origin end -offset 0 -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab_time.txt ; 2021-02-16.163434 grep -v ";" D7/regulonD7.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 $RSAT/perl-scripts/lib/color_palettes/1nt-1str_colors.tab -title 'Nucleotide composition profiles; test sequence; D7/regulonD7.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250 -ymin 0 -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.png ; 2021-02-16.163434 time ($RSAT/perl-scripts/position-analysis -v 1 -i D7/regulonD7.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 'D7/regulonD7.rm.fna' -origin end -offset 0 -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab_time.txt ; 2021-02-16.163438 grep -v ";" D7/regulonD7.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; D7/regulonD7.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250 -ymin 0 -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.png ; 2021-02-16.163438 $RSAT/perl-scripts/convert-seq -i Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna -from fasta -to fasta -mask non-dna -o D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl.fasta ; 2021-02-16.163443 $RSAT/perl-scripts/purge-sequence -dna -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl.fasta -ml 40 -mis 3 -o D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta ; 2021-02-16.164807 $RSAT/perl-scripts/sequence-lengths -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -o D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen.tab -ci 20 -o D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.tab ; 2021-02-16.164810 $RSAT/perl-scripts/XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; D7/regulonD7.rm.fna' -xsize 700 -xcol 3 -xleg1 'Peak length' -ysize 250 -ycol 4 -yleg1 'Number of peaks' -xmin 0 -ymin 0 -xgstep2 20 -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.tab -o D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.png ; 2021-02-16.164810 time ($RSAT/bin/count-words -v 1 -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -l 1 -1str > D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab_time.txt ; 2021-02-16.164811 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png ; 2021-02-16.164811 time ($RSAT/bin/count-words -v 1 -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -l 2 -1str > D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab_time.txt ; 2021-02-16.164812 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions -i D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png ; 2021-02-16.164813 time ($RSAT/perl-scripts/position-analysis -v 1 -i D7/regulonD7.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 'D7/regulonD7.rm.fna' -origin end -offset 0 -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab_time.txt ; 2021-02-16.165401 grep -v ";" D7/regulonD7.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 $RSAT/perl-scripts/lib/color_palettes/1nt-1str_colors.tab -title 'Nucleotide composition profiles; ctrl sequence; D7/regulonD7.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250 -ymin 0 -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.png ; 2021-02-16.165401 time ($RSAT/perl-scripts/position-analysis -v 1 -i D7/regulonD7.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 'D7/regulonD7.rm.fna' -origin end -offset 0 -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab_time.txt ; 2021-02-16.170040 grep -v ";" D7/regulonD7.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; D7/regulonD7.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250 -ymin 0 -o D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.png ; 2021-02-16.170040 $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 5 -o D7/regulonD7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_5nt-2str-noov.tab ; 2021-02-16.170045 $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 6 -o D7/regulonD7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab ; 2021-02-16.170051 $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 7 -o D7/regulonD7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab ; 2021-02-16.170059 $RSAT/perl-scripts/dyad-analysis -v 1 -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -quick -format fasta -return occ,freq -2str -noov -seqtype dna -l 3 -sp 0-20 -o D7/regulonD7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab ; 2021-02-16.170216 time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_5nt-2str-noov.tab -pseudo 0.01 -o D7/regulonD7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos-2str-noov_5nt_test_vs_ctrl.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos-2str-noov_5nt_test_vs_ctrl.tab_time.txt ; 2021-02-16.170217 time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 6 -expfreq D7/regulonD7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab -pseudo 0.01 -o D7/regulonD7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab_time.txt ; 2021-02-16.170218 time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab -pseudo 0.01 -o D7/regulonD7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab_time.txt ; 2021-02-16.170221 cat D7/regulonD7.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos-2str-noov_5nt_test_vs_ctrl.tab D7/regulonD7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab D7/regulonD7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab> D7/regulonD7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2.tab ; 2021-02-16.170221 time ($RSAT/perl-scripts/matrix-from-patterns -v 1 -sites -seq D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -pl D7/regulonD7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2.tab -bgfile D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_5-7nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o D7/regulonD7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm) >& D7/regulonD7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_time.txt ; 2021-02-16.170226 time ($RSAT/perl-scripts/dyad-analysis -v 1 -i D7/regulonD7.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 D7/regulonD7.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' >D7/regulonD7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab_time.txt ; 2021-02-16.170240 time ($RSAT/perl-scripts/matrix-from-patterns -v 1 -sites -seq D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -pl D7/regulonD7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -bgfile D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm) >& D7/regulonD7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_time.txt ; 2021-02-16.170245 rm -f D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf; cat D7/regulonD7.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf >> D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf; cat D7/regulonD7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf >> D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf ; 2021-02-16.170246 $RSAT/perl-scripts/convert-matrix -v 0 -i D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1.tf -from transfac -to tab -return counts -o D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1.tab ; 2021-02-16.170246 $RSAT/perl-scripts/convert-matrix -v 0 -i D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/peaks_oligos_5-7nt_m2.tf -from transfac -to tab -return counts -o D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/peaks_oligos_5-7nt_m2.tab ; 2021-02-16.170246 $RSAT/perl-scripts/convert-matrix -v 0 -i D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/peaks_oligos_5-7nt_m3.tf -from transfac -to tab -return counts -o D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/peaks_oligos_5-7nt_m3.tab ; 2021-02-16.170246 $RSAT/perl-scripts/convert-matrix -v 0 -i D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/peaks_oligos_5-7nt_m4.tf -from transfac -to tab -return counts -o D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/peaks_oligos_5-7nt_m4.tab ; 2021-02-16.170247 $RSAT/perl-scripts/convert-matrix -v 0 -i D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tab ; 2021-02-16.170247 $RSAT/perl-scripts/convert-matrix -v 0 -i D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tab ; 2021-02-16.170247 $RSAT/perl-scripts/convert-matrix -v 0 -i D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tab ; 2021-02-16.170247 $RSAT/perl-scripts/convert-matrix -v 0 -i D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tab ; 2021-02-16.170248 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1_vs_db_footDB ; 2021-02-16.170252 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/peaks_oligos_5-7nt_m2_vs_db_footDB ; 2021-02-16.170256 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/peaks_oligos_5-7nt_m3_vs_db_footDB ; 2021-02-16.170301 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/peaks_oligos_5-7nt_m4_vs_db_footDB ; 2021-02-16.170305 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footDB ; 2021-02-16.170309 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footDB ; 2021-02-16.170314 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_db_footDB ; 2021-02-16.170318 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_db_footDB ; 2021-02-16.170323 time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab) >& D7/regulonD7.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab_time.txt ; 2021-02-16.170330 $RSAT/perl-scripts/convert-graph -i D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.gml ; peak-motifs -i D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm -title D7/regulonD7.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 D7/regulonD7.rm.fna ; Directories ; output D7/regulonD7.rm.fna.peaks-rm/ ; oligos_5-7nt_m1 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/ ; oligos_5-7nt_m2 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/ ; oligos_5-7nt_m3 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/ ; oligos_5-7nt_m4 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/ ; dyads_test_vs_ctrl_m1 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/ ; dyads_test_vs_ctrl_m2 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/ ; dyads_test_vs_ctrl_m3 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/ ; dyads_test_vs_ctrl_m4 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/ ; Output files ; 1nt_ctrl_freq D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab ; 1nt_ctrl_heatmap D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png ; 1nt_ctrl_inclusive D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt ; 1nt_ctrl_profiles D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab ; 1nt_ctrl_profiles_graph D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.png ; 1nt_ctrl_profiles_index D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20_graph_index.html ; 1nt_ctrl_transitions D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab ; 1nt_test_freq D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab ; 1nt_test_heatmap D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png ; 1nt_test_inclusive D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_1nt.txt ; 1nt_test_profiles D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab ; 1nt_test_profiles_graph D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.png ; 1nt_test_profiles_index D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20_graph_index.html ; 1nt_test_transitions D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab ; 2nt_ctrl_freq D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab ; 2nt_ctrl_heatmap D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png ; 2nt_ctrl_inclusive D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_2nt.txt ; 2nt_ctrl_profiles D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab ; 2nt_ctrl_profiles_graph D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.png ; 2nt_ctrl_profiles_index D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20_graph_index.html ; 2nt_ctrl_transitions D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab ; 2nt_test_freq D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab ; 2nt_test_heatmap D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_2nt.png ; 2nt_test_inclusive D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt ; 2nt_test_profiles D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab ; 2nt_test_profiles_graph D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.png ; 2nt_test_profiles_index D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20_graph_index.html ; 2nt_test_transitions D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab ; archive D7/regulonD7.rm.fna.peaks-rm/peaks_archive.zip ; ctrl_converted D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl.fasta ; ctrl_purged D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta ; ctrl_seqlen D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen.tab ; ctrl_seqlen_distrib D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.tab ; ctrl_seqlen_distrib_graph D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.png ; dyads_test_vs_ctrl D7/regulonD7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab ; dyads_test_vs_ctrl_2pssm D7/regulonD7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt ; 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oligos_6nt_test_vs_ctrl D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab ; oligos_7nt_test_vs_ctrl D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab ; small_summary D7/regulonD7.rm.fna.peaks-rm/peaks_small_summary.html ; small_summary_txt D7/regulonD7.rm.fna.peaks-rm/reports/peaks_small_summary.txt ; synthesis D7/regulonD7.rm.fna.peaks-rm/peaks_synthesis.html ; test_converted D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test.fasta ; test_purged D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta ; test_seqlen D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen.tab ; test_seqlen_distrib D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.tab ; test_seqlen_distrib_graph D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.png ; timelog D7/regulonD7.rm.fna.peaks-rm/reports/peaks_timelog.txt ; timelog_html D7/regulonD7.rm.fna.peaks-rm/reports/peaks_timelog.html ; timetable D7/regulonD7.rm.fna.peaks-rm/reports/peaks_timetable.txt ; 2021-02-16.170419 rm -f D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta ; 2021-02-16.170419 rm -f D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta ; 2021-02-16.170419 rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg D7/regulonD7.rm.fna.peaks-rm/images_html ; peak-motifs -i D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm -title D7/regulonD7.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 D7/regulonD7.rm.fna ; Directories ; output D7/regulonD7.rm.fna.peaks-rm/ ; oligos_5-7nt_m1 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/ ; oligos_5-7nt_m2 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/ ; oligos_5-7nt_m3 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/ ; oligos_5-7nt_m4 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/ ; dyads_test_vs_ctrl_m1 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/ ; dyads_test_vs_ctrl_m2 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/ ; dyads_test_vs_ctrl_m3 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/ ; dyads_test_vs_ctrl_m4 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/ ; Output files ; 1nt_ctrl_freq D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab ; 1nt_ctrl_heatmap D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png ; 1nt_ctrl_inclusive D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt ; 1nt_ctrl_profiles D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab ; 1nt_ctrl_profiles_graph D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.png ; 1nt_ctrl_profiles_index D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20_graph_index.html ; 1nt_ctrl_transitions D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab ; 1nt_test_freq D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab ; 1nt_test_heatmap D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png ; 1nt_test_inclusive D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_1nt.txt ; 1nt_test_profiles D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab ; 1nt_test_profiles_graph D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.png ; 1nt_test_profiles_index D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20_graph_index.html ; 1nt_test_transitions D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab ; 2nt_ctrl_freq D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab ; 2nt_ctrl_heatmap D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png ; 2nt_ctrl_inclusive D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_2nt.txt ; 2nt_ctrl_profiles D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab ; 2nt_ctrl_profiles_graph D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.png ; 2nt_ctrl_profiles_index D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20_graph_index.html ; 2nt_ctrl_transitions D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab ; 2nt_test_freq D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab ; 2nt_test_heatmap D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_2nt.png ; 2nt_test_inclusive D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt ; 2nt_test_profiles D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab ; 2nt_test_profiles_graph D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.png ; 2nt_test_profiles_index D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20_graph_index.html ; 2nt_test_transitions D7/regulonD7.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab ; archive D7/regulonD7.rm.fna.peaks-rm/peaks_archive.zip ; ctrl_converted D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl.fasta ; ctrl_purged D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta ; ctrl_seqlen D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen.tab ; ctrl_seqlen_distrib D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.tab ; ctrl_seqlen_distrib_graph D7/regulonD7.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.png ; dyads_test_vs_ctrl D7/regulonD7.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab ; dyads_test_vs_ctrl_2pssm D7/regulonD7.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 D7/regulonD7.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 D7/regulonD7.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 D7/regulonD7.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 D7/regulonD7.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 D7/regulonD7.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 D7/regulonD7.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 D7/regulonD7.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 D7/regulonD7.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 D7/regulonD7.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 D7/regulonD7.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 D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites_per_peak.png ; dyads_test_vs_ctrl_m1_tab D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tab ; dyads_test_vs_ctrl_m1_tf D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tf ; dyads_test_vs_ctrl_m1_vs_db_footDB D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footDB.tab ; dyads_test_vs_ctrl_m1_vs_db_footDB_html D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footDB.html ; dyads_test_vs_ctrl_m1_vs_ref D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_ref.tab ; dyads_test_vs_ctrl_m1_vs_ref_html D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_ref.html ; dyads_test_vs_ctrl_m2_logo D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_logo.png ; dyads_test_vs_ctrl_m2_logo_rc D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_logo_rc.png ; dyads_test_vs_ctrl_m2_pssm_enrichment D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_scan_mkv1_enrichment.tab ; dyads_test_vs_ctrl_m2_pssm_enrichment_png D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_scan_mkv1_enrichment.png ; dyads_test_vs_ctrl_m2_pssm_site_distrib D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_site_distrib.tab ; dyads_test_vs_ctrl_m2_pssm_site_distrib_graph D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_site_distrib.png ; dyads_test_vs_ctrl_m2_pssm_sites D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_sites.tab ; dyads_test_vs_ctrl_m2_pssm_sites_per_peak D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_sites_per_peak.tab ; dyads_test_vs_ctrl_m2_pssm_sites_per_peak_graph D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_sites_per_peak.png ; dyads_test_vs_ctrl_m2_tab D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tab ; dyads_test_vs_ctrl_m2_tf D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tf ; dyads_test_vs_ctrl_m2_vs_db_footDB D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footDB.tab ; dyads_test_vs_ctrl_m2_vs_db_footDB_html D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footDB.html ; dyads_test_vs_ctrl_m2_vs_ref D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_ref.tab ; dyads_test_vs_ctrl_m2_vs_ref_html D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_ref.html ; dyads_test_vs_ctrl_m3_logo D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_logo.png ; dyads_test_vs_ctrl_m3_logo_rc D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_logo_rc.png ; dyads_test_vs_ctrl_m3_pssm_enrichment D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_scan_mkv1_enrichment.tab ; dyads_test_vs_ctrl_m3_pssm_enrichment_png D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_scan_mkv1_enrichment.png ; dyads_test_vs_ctrl_m3_pssm_site_distrib D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_site_distrib.tab ; dyads_test_vs_ctrl_m3_pssm_site_distrib_graph D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_site_distrib.png ; dyads_test_vs_ctrl_m3_pssm_sites D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_sites.tab ; dyads_test_vs_ctrl_m3_pssm_sites_per_peak D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_sites_per_peak.tab ; dyads_test_vs_ctrl_m3_pssm_sites_per_peak_graph D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_sites_per_peak.png ; dyads_test_vs_ctrl_m3_tab D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tab ; dyads_test_vs_ctrl_m3_tf D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tf ; dyads_test_vs_ctrl_m3_vs_db_footDB D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_db_footDB.tab ; dyads_test_vs_ctrl_m3_vs_db_footDB_html D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_db_footDB.html ; dyads_test_vs_ctrl_m3_vs_ref D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_ref.tab ; dyads_test_vs_ctrl_m3_vs_ref_html D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_ref.html ; dyads_test_vs_ctrl_m4_logo D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_logo.png ; dyads_test_vs_ctrl_m4_logo_rc D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_logo_rc.png ; dyads_test_vs_ctrl_m4_pssm_enrichment D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_scan_mkv1_enrichment.tab ; dyads_test_vs_ctrl_m4_pssm_enrichment_png D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_scan_mkv1_enrichment.png ; dyads_test_vs_ctrl_m4_pssm_site_distrib D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_site_distrib.tab ; dyads_test_vs_ctrl_m4_pssm_site_distrib_graph D7/regulonD7.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_site_distrib.png ; 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