; 2023-05-30.162352
peak-motifs  -i regulonM11_up4.rm.fna -ctrl Prunus_persica.Prunus_persica_NCBIv2.38-up4.rm.fna -motif_db footprintDB-plants transfac ../public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -prefix peaks -outdir peaks-rm-orig -title analysis_M11 -origin end -disco oligos,dyads -nmotifs 6 -minol 6 -maxol 8 -scan_markov 1 -noov -img_format png -task purge,seqlen,composition,disco,merge_motifs,split_motifs,timelog,motifs_vs_db,synthesis,small_summary,clean_seq



; 2023-05-30.162352
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  peaks-rm-orig/images_html


; 2023-05-30.162352
rsat convert-seq -i regulonM11_up4.rm.fna -from fasta -to fasta -mask non-dna -o peaks-rm-orig/data/sequences/peaks_test.fasta


; 2023-05-30.162353
rsat purge-sequence -dna -i peaks-rm-orig/data/sequences/peaks_test.fasta -ml 40 -mis 3 -o peaks-rm-orig/data/sequences/peaks_test_purged_ml40_mis3.fasta


; 2023-05-30.162354
rsat sequence-lengths -i peaks-rm-orig/data/sequences/peaks_test_purged_ml40_mis3.fasta -o peaks-rm-orig/data/sequences/peaks_test_seqlen.tab ; rsat classfreq -v 1 -col 2 -i peaks-rm-orig/data/sequences/peaks_test_seqlen.tab -ci 20 -o peaks-rm-orig/data/sequences/peaks_test_seqlen_distrib.tab


; 2023-05-30.162354
rsat XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; analysis_M11' -xsize 700 -xcol 3 -xleg1 'Peak length' -ysize 250 -ycol 4 -yleg1 'Number of peaks' -xmin 0 -ymin 0 -xgstep2 20 -i peaks-rm-orig/data/sequences/peaks_test_seqlen_distrib.tab -o peaks-rm-orig/data/sequences/peaks_test_seqlen_distrib.png


; 2023-05-30.162354
time -o peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_1nt.tab_time.txt rsat count-words -v 1 -i peaks-rm-orig/data/sequences/peaks_test_purged_ml40_mis3.fasta -l 1 -1str > peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_1nt.tab


; 2023-05-30.162355
rsat convert-background-model -from oligos -to inclusive  -i peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_1nt.tab -o peaks-rm-orig/results/composition/peaks_test_inclusive-1str-ovlp_1nt.txt; rsat convert-background-model -from oligos -to transitions  -i peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_1nt.tab -o peaks-rm-orig/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 peaks-rm-orig/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab | rsat draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o peaks-rm-orig/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png


; 2023-05-30.162355
time -o peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_2nt.tab_time.txt rsat count-words -v 1 -i peaks-rm-orig/data/sequences/peaks_test_purged_ml40_mis3.fasta -l 2 -1str > peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_2nt.tab


; 2023-05-30.162356
rsat convert-background-model -from oligos -to inclusive  -i peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_2nt.tab -o peaks-rm-orig/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt; rsat convert-background-model -from oligos -to transitions  -i peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_2nt.tab -o peaks-rm-orig/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 peaks-rm-orig/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab | rsat draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o peaks-rm-orig/results/composition/peaks_test_heatmap-1str-ovlp_2nt.png


; 2023-05-30.162356
time -o peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab_time.txt rsat position-analysis -v 1 -i peaks-rm-orig/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 'analysis_M11' -origin end -offset 0 -o peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab


; 2023-05-30.162358
grep -v ";" peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | rsat 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; analysis_M11' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.png


; 2023-05-30.162359
time -o peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab_time.txt rsat position-analysis -v 1 -i peaks-rm-orig/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 'analysis_M11' -origin end -offset 0 -o peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab


; 2023-05-30.162403
grep -v ";" peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | rsat 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; analysis_M11' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.png


; 2023-05-30.162403
rsat convert-seq -i Prunus_persica.Prunus_persica_NCBIv2.38-up4.rm.fna -from fasta -to fasta -mask non-dna -o peaks-rm-orig/data/sequences/peaks_ctrl.fasta


; 2023-05-30.162404
rsat purge-sequence -dna -i peaks-rm-orig/data/sequences/peaks_ctrl.fasta -ml 40 -mis 3 -o peaks-rm-orig/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta


; 2023-05-30.162433
rsat sequence-lengths -i peaks-rm-orig/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -o peaks-rm-orig/data/sequences/peaks_ctrl_seqlen.tab ; rsat classfreq -v 1 -col 2 -i peaks-rm-orig/data/sequences/peaks_ctrl_seqlen.tab -ci 20 -o peaks-rm-orig/data/sequences/peaks_ctrl_seqlen_distrib.tab


; 2023-05-30.162433
rsat XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; analysis_M11' -xsize 700 -xcol 3 -xleg1 'Peak length' -ysize 250 -ycol 4 -yleg1 'Number of peaks' -xmin 0 -ymin 0 -xgstep2 20 -i peaks-rm-orig/data/sequences/peaks_ctrl_seqlen_distrib.tab -o peaks-rm-orig/data/sequences/peaks_ctrl_seqlen_distrib.png


; 2023-05-30.162434
time -o peaks-rm-orig/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab_time.txt rsat count-words -v 1 -i peaks-rm-orig/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -l 1 -1str > peaks-rm-orig/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab


; 2023-05-30.162434
rsat convert-background-model -from oligos -to inclusive  -i peaks-rm-orig/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab -o peaks-rm-orig/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt; rsat convert-background-model -from oligos -to transitions  -i peaks-rm-orig/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab -o peaks-rm-orig/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 peaks-rm-orig/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab | rsat draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o peaks-rm-orig/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png


; 2023-05-30.162435
time -o peaks-rm-orig/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab_time.txt rsat count-words -v 1 -i peaks-rm-orig/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -l 2 -1str > peaks-rm-orig/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab


; 2023-05-30.162435
rsat convert-background-model -from oligos -to inclusive  -i peaks-rm-orig/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab -o peaks-rm-orig/results/composition/peaks_ctrl_inclusive-1str-ovlp_2nt.txt; rsat convert-background-model -from oligos -to transitions  -i peaks-rm-orig/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab -o peaks-rm-orig/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 peaks-rm-orig/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab | rsat draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o peaks-rm-orig/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png


; 2023-05-30.162436
time -o peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab_time.txt rsat position-analysis -v 1 -i peaks-rm-orig/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 'analysis_M11' -origin end -offset 0 -o peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab


; 2023-05-30.162505
grep -v ";" peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | rsat 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; analysis_M11' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.png


; 2023-05-30.162505
time -o peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab_time.txt rsat position-analysis -v 1 -i peaks-rm-orig/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 'analysis_M11' -origin end -offset 0 -o peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab


; 2023-05-30.162541
grep -v ";" peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | rsat 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; analysis_M11' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.png


; 2023-05-30.162541
rsat oligo-analysis -v 1 -quick -i peaks-rm-orig/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 6 -o peaks-rm-orig/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab


; 2023-05-30.162543
rsat oligo-analysis -v 1 -quick -i peaks-rm-orig/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 7 -o peaks-rm-orig/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab


; 2023-05-30.162545
rsat oligo-analysis -v 1 -quick -i peaks-rm-orig/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 8 -o peaks-rm-orig/results/oligos_8nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_8nt-2str-noov.tab


; 2023-05-30.162550
rsat dyad-analysis -v 1 -i peaks-rm-orig/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -quick -format fasta -return occ,freq -2str -noov -seqtype dna -l 3 -sp 0-20  -o peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab


; 2023-05-30.162604
time -o peaks-rm-orig/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab_time.txt rsat oligo-analysis -v 1 -quick -i peaks-rm-orig/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 peaks-rm-orig/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab -pseudo 0.01 -o peaks-rm-orig/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab


; 2023-05-30.162605
time -o peaks-rm-orig/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab_time.txt rsat oligo-analysis -v 1 -quick -i peaks-rm-orig/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 peaks-rm-orig/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab -pseudo 0.01 -o peaks-rm-orig/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab


; 2023-05-30.162607
time -o peaks-rm-orig/results/oligos_8nt_test_vs_ctrl/peaks_oligos-2str-noov_8nt_test_vs_ctrl.tab_time.txt rsat oligo-analysis -v 1 -quick -i peaks-rm-orig/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 8 -expfreq peaks-rm-orig/results/oligos_8nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_8nt-2str-noov.tab -pseudo 0.01 -o peaks-rm-orig/results/oligos_8nt_test_vs_ctrl/peaks_oligos-2str-noov_8nt_test_vs_ctrl.tab


; 2023-05-30.162611
cat peaks-rm-orig/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab peaks-rm-orig/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab peaks-rm-orig/results/oligos_8nt_test_vs_ctrl/peaks_oligos-2str-noov_8nt_test_vs_ctrl.tab> peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2.tab


; 2023-05-30.162611
time -o peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_time.txt rsat matrix-from-patterns -v 1  -sites -seq peaks-rm-orig/data/sequences/peaks_test.fasta -pl peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2.tab -bgfile peaks-rm-orig/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 6 -max_asmb_width 20 -subst 1 -prefix oligos_6-8nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm


; 2023-05-30.162618
time -o peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab_time.txt rsat dyad-analysis -v 1 -i peaks-rm-orig/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 peaks-rm-orig/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' >peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab


; 2023-05-30.162624
time -o peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_time.txt rsat matrix-from-patterns -v 1  -sites -seq peaks-rm-orig/data/sequences/peaks_test.fasta -pl peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -bgfile peaks-rm-orig/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 6 -max_asmb_width 20 -subst 1 -prefix dyads_test_vs_ctrl -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm


; 2023-05-30.162632
rm -f peaks-rm-orig/results/discovered_motifs/peaks_motifs_discovered.tf; cat peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices.tf >> peaks-rm-orig/results/discovered_motifs/peaks_motifs_discovered.tf; cat peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf >> peaks-rm-orig/results/discovered_motifs/peaks_motifs_discovered.tf


; 2023-05-30.162632
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m1/peaks_oligos_6-8nt_m1.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m1/peaks_oligos_6-8nt_m1.tab


; 2023-05-30.162633
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2.tab


; 2023-05-30.162633
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3.tab


; 2023-05-30.162633
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4.tab


; 2023-05-30.162633
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5.tab


; 2023-05-30.162634
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6.tab


; 2023-05-30.162634
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tab


; 2023-05-30.162634
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tab


; 2023-05-30.162635
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tab


; 2023-05-30.162635
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tab


; 2023-05-30.162635
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tab


; 2023-05-30.162636
rsat convert-matrix -v 0 -i peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6.tf -from transfac -to tab -return counts -o peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6.tab


; 2023-05-30.162636
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m1/peaks_oligos_6-8nt_m1.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m1/peaks_oligos_6-8nt_m1_vs_db_footprintDB-plants


; 2023-05-30.162637
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2_vs_db_footprintDB-plants


; 2023-05-30.162639
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_vs_db_footprintDB-plants


; 2023-05-30.162641
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_vs_db_footprintDB-plants


; 2023-05-30.162643
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_vs_db_footprintDB-plants


; 2023-05-30.162644
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_vs_db_footprintDB-plants


; 2023-05-30.162646
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footprintDB-plants


; 2023-05-30.162648
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footprintDB-plants


; 2023-05-30.162649
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_db_footprintDB-plants


; 2023-05-30.162651
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_db_footprintDB-plants


; 2023-05-30.162653
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_vs_db_footprintDB-plants


; 2023-05-30.162655
rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_vs_db_footprintDB-plants


; 2023-05-30.162657
time -o peaks-rm-orig/results/discovered_vs_db/peaks_motifs_vs_db_footprintDB-plants.tab_time.txt rsat compare-matrices -v 1 -mode matches -format1 transfac -file1 peaks-rm-orig/results/discovered_motifs/peaks_motifs_discovered.tf -format2 transfac -file2 ../public_html/motif_databases/footprintDB/footprintDB.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 peaks-rm-orig/results/discovered_vs_db/peaks_motifs_vs_db_footprintDB-plants.tab


; 2023-05-30.162659
$RSAT/perl-scripts/convert-graph -i peaks-rm-orig/results/discovered_vs_db/peaks_motifs_vs_db_footprintDB-plants.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o peaks-rm-orig/results/discovered_vs_db/peaks_motifs_vs_db_footprintDB-plants.gml


; 2023-05-30.162705
$RSAT/perl-scripts/text-to-html -font variable -i peaks-rm-orig/reports/peaks_timelog.txt -o peaks-rm-orig/reports/peaks_timelog.html

; peak-motifs  -i regulonM11_up4.rm.fna -ctrl Prunus_persica.Prunus_persica_NCBIv2.38-up4.rm.fna -motif_db footprintDB-plants transfac ../public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -prefix peaks -outdir peaks-rm-orig -title analysis_M11 -origin end -disco oligos,dyads -nmotifs 6 -minol 6 -maxol 8 -scan_markov 1 -noov -img_format png -task purge,seqlen,composition,disco,merge_motifs,split_motifs,timelog,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         	6
;	oligo_max_len         	8
;	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        	6
; Input files
;	ctrl_seq              	Prunus_persica.Prunus_persica_NCBIv2.38-up4.rm.fna
;	motif_db_footprintDB-plants	../public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
;	test_seq              	regulonM11_up4.rm.fna
; Directories
;	output                        	peaks-rm-orig/
;	oligos_6-8nt_m1               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m1/
;	oligos_6-8nt_m2               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/
;	oligos_6-8nt_m3               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/
;	oligos_6-8nt_m4               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/
;	oligos_6-8nt_m5               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/
;	oligos_6-8nt_m6               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/
;	dyads_test_vs_ctrl_m1         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/
;	dyads_test_vs_ctrl_m2         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/
;	dyads_test_vs_ctrl_m3         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/
;	dyads_test_vs_ctrl_m4         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/
;	dyads_test_vs_ctrl_m5         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/
;	dyads_test_vs_ctrl_m6         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/
; Output files
;	1nt_ctrl_freq                 	peaks-rm-orig/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab
;	1nt_ctrl_heatmap              	peaks-rm-orig/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png
;	1nt_ctrl_inclusive            	peaks-rm-orig/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt
;	1nt_ctrl_profiles             	peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_ctrl_profiles_graph       	peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.png
;	1nt_ctrl_profiles_index       	peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_ctrl_transitions          	peaks-rm-orig/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab
;	1nt_test_freq                 	peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	peaks-rm-orig/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	peaks-rm-orig/results/composition/peaks_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_test_transitions          	peaks-rm-orig/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab
;	2nt_ctrl_freq                 	peaks-rm-orig/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab
;	2nt_ctrl_heatmap              	peaks-rm-orig/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png
;	2nt_ctrl_inclusive            	peaks-rm-orig/results/composition/peaks_ctrl_inclusive-1str-ovlp_2nt.txt
;	2nt_ctrl_profiles             	peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_ctrl_profiles_graph       	peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.png
;	2nt_ctrl_profiles_index       	peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_ctrl_transitions          	peaks-rm-orig/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab
;	2nt_test_freq                 	peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	peaks-rm-orig/results/composition/peaks_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	peaks-rm-orig/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_test_transitions          	peaks-rm-orig/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab
;	archive                       	peaks-rm-orig/peaks_archive.zip
;	ctrl_converted                	peaks-rm-orig/data/sequences/peaks_ctrl.fasta
;	ctrl_purged                   	peaks-rm-orig/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta
;	ctrl_seqlen                   	peaks-rm-orig/data/sequences/peaks_ctrl_seqlen.tab
;	ctrl_seqlen_distrib           	peaks-rm-orig/data/sequences/peaks_ctrl_seqlen_distrib.tab
;	ctrl_seqlen_distrib_graph     	peaks-rm-orig/data/sequences/peaks_ctrl_seqlen_distrib.png
;	dyads_test_vs_ctrl            	peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_test_vs_ctrl_2pssm      	peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt
;	dyads_test_vs_ctrl_asmb       	peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
;	dyads_test_vs_ctrl_bg_file    	peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_test_vs_ctrl_m1_logo    	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_logo.png
;	dyads_test_vs_ctrl_m1_logo_rc 	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_logo_rc.png
;	dyads_test_vs_ctrl_m1_pssm_enrichment	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_site_distrib.png
;	dyads_test_vs_ctrl_m1_pssm_sites	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites_per_peak.png
;	dyads_test_vs_ctrl_m1_tab     	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tab
;	dyads_test_vs_ctrl_m1_tf      	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tf
;	dyads_test_vs_ctrl_m1_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footprintDB-plants.tab
;	dyads_test_vs_ctrl_m1_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footprintDB-plants.html
;	dyads_test_vs_ctrl_m1_vs_ref  	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_ref.html
;	dyads_test_vs_ctrl_m2_logo    	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_logo.png
;	dyads_test_vs_ctrl_m2_logo_rc 	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_logo_rc.png
;	dyads_test_vs_ctrl_m2_pssm_enrichment	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_site_distrib.png
;	dyads_test_vs_ctrl_m2_pssm_sites	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_sites_per_peak.png
;	dyads_test_vs_ctrl_m2_tab     	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tab
;	dyads_test_vs_ctrl_m2_tf      	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tf
;	dyads_test_vs_ctrl_m2_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footprintDB-plants.tab
;	dyads_test_vs_ctrl_m2_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footprintDB-plants.html
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;	oligos_6-8nt_m2_pssm_enrichment_png	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2_scan_mkv1_enrichment.png
;	oligos_6-8nt_m2_pssm_site_distrib	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2_site_distrib.tab
;	oligos_6-8nt_m2_pssm_site_distrib_graph	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2_site_distrib.png
;	oligos_6-8nt_m2_pssm_sites    	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2_sites.tab
;	oligos_6-8nt_m2_pssm_sites_per_peak	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2_sites_per_peak.tab
;	oligos_6-8nt_m2_pssm_sites_per_peak_graph	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2_sites_per_peak.png
;	oligos_6-8nt_m2_tab           	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2.tab
;	oligos_6-8nt_m2_tf            	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2.tf
;	oligos_6-8nt_m2_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2_vs_db_footprintDB-plants.tab
;	oligos_6-8nt_m2_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2_vs_db_footprintDB-plants.html
;	oligos_6-8nt_m2_vs_ref        	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2_vs_ref.tab
;	oligos_6-8nt_m2_vs_ref_html   	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/peaks_oligos_6-8nt_m2_vs_ref.html
;	oligos_6-8nt_m3_logo          	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_logo.png
;	oligos_6-8nt_m3_logo_rc       	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_logo_rc.png
;	oligos_6-8nt_m3_pssm_enrichment	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_scan_mkv1_enrichment.tab
;	oligos_6-8nt_m3_pssm_enrichment_png	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_scan_mkv1_enrichment.png
;	oligos_6-8nt_m3_pssm_site_distrib	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_site_distrib.tab
;	oligos_6-8nt_m3_pssm_site_distrib_graph	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_site_distrib.png
;	oligos_6-8nt_m3_pssm_sites    	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_sites.tab
;	oligos_6-8nt_m3_pssm_sites_per_peak	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_sites_per_peak.tab
;	oligos_6-8nt_m3_pssm_sites_per_peak_graph	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_sites_per_peak.png
;	oligos_6-8nt_m3_tab           	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3.tab
;	oligos_6-8nt_m3_tf            	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3.tf
;	oligos_6-8nt_m3_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_vs_db_footprintDB-plants.tab
;	oligos_6-8nt_m3_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_vs_db_footprintDB-plants.html
;	oligos_6-8nt_m3_vs_ref        	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_vs_ref.tab
;	oligos_6-8nt_m3_vs_ref_html   	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/peaks_oligos_6-8nt_m3_vs_ref.html
;	oligos_6-8nt_m4_logo          	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_logo.png
;	oligos_6-8nt_m4_logo_rc       	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_logo_rc.png
;	oligos_6-8nt_m4_pssm_enrichment	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_scan_mkv1_enrichment.tab
;	oligos_6-8nt_m4_pssm_enrichment_png	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_scan_mkv1_enrichment.png
;	oligos_6-8nt_m4_pssm_site_distrib	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_site_distrib.tab
;	oligos_6-8nt_m4_pssm_site_distrib_graph	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_site_distrib.png
;	oligos_6-8nt_m4_pssm_sites    	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_sites.tab
;	oligos_6-8nt_m4_pssm_sites_per_peak	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_sites_per_peak.tab
;	oligos_6-8nt_m4_pssm_sites_per_peak_graph	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_sites_per_peak.png
;	oligos_6-8nt_m4_tab           	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4.tab
;	oligos_6-8nt_m4_tf            	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4.tf
;	oligos_6-8nt_m4_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_vs_db_footprintDB-plants.tab
;	oligos_6-8nt_m4_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_vs_db_footprintDB-plants.html
;	oligos_6-8nt_m4_vs_ref        	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_vs_ref.tab
;	oligos_6-8nt_m4_vs_ref_html   	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/peaks_oligos_6-8nt_m4_vs_ref.html
;	oligos_6-8nt_m5_logo          	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_logo.png
;	oligos_6-8nt_m5_logo_rc       	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_logo_rc.png
;	oligos_6-8nt_m5_pssm_enrichment	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_scan_mkv1_enrichment.tab
;	oligos_6-8nt_m5_pssm_enrichment_png	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_scan_mkv1_enrichment.png
;	oligos_6-8nt_m5_pssm_site_distrib	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_site_distrib.tab
;	oligos_6-8nt_m5_pssm_site_distrib_graph	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_site_distrib.png
;	oligos_6-8nt_m5_pssm_sites    	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_sites.tab
;	oligos_6-8nt_m5_pssm_sites_per_peak	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_sites_per_peak.tab
;	oligos_6-8nt_m5_pssm_sites_per_peak_graph	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_sites_per_peak.png
;	oligos_6-8nt_m5_tab           	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5.tab
;	oligos_6-8nt_m5_tf            	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5.tf
;	oligos_6-8nt_m5_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_vs_db_footprintDB-plants.tab
;	oligos_6-8nt_m5_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_vs_db_footprintDB-plants.html
;	oligos_6-8nt_m5_vs_ref        	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_vs_ref.tab
;	oligos_6-8nt_m5_vs_ref_html   	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/peaks_oligos_6-8nt_m5_vs_ref.html
;	oligos_6-8nt_m6_logo          	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_logo.png
;	oligos_6-8nt_m6_logo_rc       	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_logo_rc.png
;	oligos_6-8nt_m6_pssm_enrichment	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_scan_mkv1_enrichment.tab
;	oligos_6-8nt_m6_pssm_enrichment_png	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_scan_mkv1_enrichment.png
;	oligos_6-8nt_m6_pssm_site_distrib	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_site_distrib.tab
;	oligos_6-8nt_m6_pssm_site_distrib_graph	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_site_distrib.png
;	oligos_6-8nt_m6_pssm_sites    	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_sites.tab
;	oligos_6-8nt_m6_pssm_sites_per_peak	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_sites_per_peak.tab
;	oligos_6-8nt_m6_pssm_sites_per_peak_graph	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_sites_per_peak.png
;	oligos_6-8nt_m6_tab           	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6.tab
;	oligos_6-8nt_m6_tf            	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6.tf
;	oligos_6-8nt_m6_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_vs_db_footprintDB-plants.tab
;	oligos_6-8nt_m6_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_vs_db_footprintDB-plants.html
;	oligos_6-8nt_m6_vs_ref        	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_vs_ref.tab
;	oligos_6-8nt_m6_vs_ref_html   	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_vs_ref.html
;	oligos_6-8nt_pssm_counts      	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices.txt
;	oligos_6-8nt_pssm_logo1       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m1.png
;	oligos_6-8nt_pssm_logo2       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m2.png
;	oligos_6-8nt_pssm_logo3       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m3.png
;	oligos_6-8nt_pssm_logo4       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m4.png
;	oligos_6-8nt_pssm_logo5       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m5.png
;	oligos_6-8nt_pssm_logo6       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m6.png
;	oligos_6-8nt_pssm_logo_rc1    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m1_rc.png
;	oligos_6-8nt_pssm_logo_rc2    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m2_rc.png
;	oligos_6-8nt_pssm_logo_rc3    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m3_rc.png
;	oligos_6-8nt_pssm_logo_rc4    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m4_rc.png
;	oligos_6-8nt_pssm_logo_rc5    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m5_rc.png
;	oligos_6-8nt_pssm_logo_rc6    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m6_rc.png
;	oligos_6-8nt_pssm_sig         	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_sig_matrices.tf
;	oligos_6-8nt_pssm_tf          	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices.tf
;	oligos_6nt_test_vs_ctrl       	peaks-rm-orig/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab
;	oligos_6nt_test_vs_ctrl_bg_file	peaks-rm-orig/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab
;	oligos_7nt_test_vs_ctrl       	peaks-rm-orig/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab
;	oligos_7nt_test_vs_ctrl_bg_file	peaks-rm-orig/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab
;	oligos_8nt_test_vs_ctrl       	peaks-rm-orig/results/oligos_8nt_test_vs_ctrl/peaks_oligos-2str-noov_8nt_test_vs_ctrl.tab
;	oligos_8nt_test_vs_ctrl_bg_file	peaks-rm-orig/results/oligos_8nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_8nt-2str-noov.tab
;	small_summary                 	peaks-rm-orig/peaks_small_summary.html
;	small_summary_txt             	peaks-rm-orig/reports/peaks_small_summary.txt
;	synthesis                     	peaks-rm-orig/peaks_synthesis.html
;	test_converted                	peaks-rm-orig/data/sequences/peaks_test.fasta
;	test_purged                   	peaks-rm-orig/data/sequences/peaks_test_purged_ml40_mis3.fasta
;	test_seqlen                   	peaks-rm-orig/data/sequences/peaks_test_seqlen.tab
;	test_seqlen_distrib           	peaks-rm-orig/data/sequences/peaks_test_seqlen_distrib.tab
;	test_seqlen_distrib_graph     	peaks-rm-orig/data/sequences/peaks_test_seqlen_distrib.png
;	timelog                       	peaks-rm-orig/reports/peaks_timelog.txt
;	timelog_html                  	peaks-rm-orig/reports/peaks_timelog.html
;	timetable                     	peaks-rm-orig/reports/peaks_timetable.txt

; 2023-05-30.162705
rm -f peaks-rm-orig/data/sequences/peaks_test_purged_ml40_mis3.fasta


; 2023-05-30.162705
rm -f peaks-rm-orig/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta


; 2023-05-30.162705
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  peaks-rm-orig/images_html

; peak-motifs  -i regulonM11_up4.rm.fna -ctrl Prunus_persica.Prunus_persica_NCBIv2.38-up4.rm.fna -motif_db footprintDB-plants transfac ../public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -prefix peaks -outdir peaks-rm-orig -title analysis_M11 -origin end -disco oligos,dyads -nmotifs 6 -minol 6 -maxol 8 -scan_markov 1 -noov -img_format png -task purge,seqlen,composition,disco,merge_motifs,split_motifs,timelog,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         	6
;	oligo_max_len         	8
;	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        	6
; Input files
;	ctrl_seq              	Prunus_persica.Prunus_persica_NCBIv2.38-up4.rm.fna
;	motif_db_footprintDB-plants	../public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
;	test_seq              	regulonM11_up4.rm.fna
; Directories
;	output                        	peaks-rm-orig/
;	oligos_6-8nt_m1               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m1/
;	oligos_6-8nt_m2               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m2/
;	oligos_6-8nt_m3               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m3/
;	oligos_6-8nt_m4               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m4/
;	oligos_6-8nt_m5               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m5/
;	oligos_6-8nt_m6               	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/
;	dyads_test_vs_ctrl_m1         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/
;	dyads_test_vs_ctrl_m2         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/
;	dyads_test_vs_ctrl_m3         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/
;	dyads_test_vs_ctrl_m4         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/
;	dyads_test_vs_ctrl_m5         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/
;	dyads_test_vs_ctrl_m6         	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/
; Output files
;	1nt_ctrl_freq                 	peaks-rm-orig/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab
;	1nt_ctrl_heatmap              	peaks-rm-orig/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png
;	1nt_ctrl_inclusive            	peaks-rm-orig/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt
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;	1nt_ctrl_transitions          	peaks-rm-orig/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab
;	1nt_test_freq                 	peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	peaks-rm-orig/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png
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;	1nt_test_profiles_index       	peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_test_transitions          	peaks-rm-orig/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab
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;	2nt_ctrl_heatmap              	peaks-rm-orig/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png
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;	2nt_ctrl_profiles_index       	peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_ctrl_transitions          	peaks-rm-orig/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab
;	2nt_test_freq                 	peaks-rm-orig/results/composition/peaks_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	peaks-rm-orig/results/composition/peaks_test_heatmap-1str-ovlp_2nt.png
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;	2nt_test_profiles             	peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	peaks-rm-orig/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_test_transitions          	peaks-rm-orig/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab
;	archive                       	peaks-rm-orig/peaks_archive.zip
;	ctrl_converted                	peaks-rm-orig/data/sequences/peaks_ctrl.fasta
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;	ctrl_seqlen                   	peaks-rm-orig/data/sequences/peaks_ctrl_seqlen.tab
;	ctrl_seqlen_distrib           	peaks-rm-orig/data/sequences/peaks_ctrl_seqlen_distrib.tab
;	ctrl_seqlen_distrib_graph     	peaks-rm-orig/data/sequences/peaks_ctrl_seqlen_distrib.png
;	dyads_test_vs_ctrl            	peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_test_vs_ctrl_2pssm      	peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt
;	dyads_test_vs_ctrl_asmb       	peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
;	dyads_test_vs_ctrl_bg_file    	peaks-rm-orig/results/dyads_test_vs_ctrl/peaks_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_test_vs_ctrl_m1_logo    	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_logo.png
;	dyads_test_vs_ctrl_m1_logo_rc 	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_logo_rc.png
;	dyads_test_vs_ctrl_m1_pssm_enrichment	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_site_distrib.png
;	dyads_test_vs_ctrl_m1_pssm_sites	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites_per_peak.png
;	dyads_test_vs_ctrl_m1_tab     	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tab
;	dyads_test_vs_ctrl_m1_tf      	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tf
;	dyads_test_vs_ctrl_m1_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footprintDB-plants.tab
;	dyads_test_vs_ctrl_m1_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footprintDB-plants.html
;	dyads_test_vs_ctrl_m1_vs_ref  	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_ref.html
;	dyads_test_vs_ctrl_m2_logo    	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_logo.png
;	dyads_test_vs_ctrl_m2_logo_rc 	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_logo_rc.png
;	dyads_test_vs_ctrl_m2_pssm_enrichment	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_site_distrib.png
;	dyads_test_vs_ctrl_m2_pssm_sites	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_sites_per_peak.png
;	dyads_test_vs_ctrl_m2_tab     	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tab
;	dyads_test_vs_ctrl_m2_tf      	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tf
;	dyads_test_vs_ctrl_m2_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footprintDB-plants.tab
;	dyads_test_vs_ctrl_m2_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footprintDB-plants.html
;	dyads_test_vs_ctrl_m2_vs_ref  	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_ref.html
;	dyads_test_vs_ctrl_m3_logo    	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_logo.png
;	dyads_test_vs_ctrl_m3_logo_rc 	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_logo_rc.png
;	dyads_test_vs_ctrl_m3_pssm_enrichment	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_site_distrib.png
;	dyads_test_vs_ctrl_m3_pssm_sites	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_sites_per_peak.png
;	dyads_test_vs_ctrl_m3_tab     	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tab
;	dyads_test_vs_ctrl_m3_tf      	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tf
;	dyads_test_vs_ctrl_m3_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_db_footprintDB-plants.tab
;	dyads_test_vs_ctrl_m3_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_db_footprintDB-plants.html
;	dyads_test_vs_ctrl_m3_vs_ref  	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_ref.html
;	dyads_test_vs_ctrl_m4_logo    	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_logo.png
;	dyads_test_vs_ctrl_m4_logo_rc 	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_logo_rc.png
;	dyads_test_vs_ctrl_m4_pssm_enrichment	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/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	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_site_distrib.png
;	dyads_test_vs_ctrl_m4_pssm_sites	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_sites.tab
;	dyads_test_vs_ctrl_m4_pssm_sites_per_peak	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_sites_per_peak.tab
;	dyads_test_vs_ctrl_m4_pssm_sites_per_peak_graph	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_sites_per_peak.png
;	dyads_test_vs_ctrl_m4_tab     	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tab
;	dyads_test_vs_ctrl_m4_tf      	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tf
;	dyads_test_vs_ctrl_m4_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_db_footprintDB-plants.tab
;	dyads_test_vs_ctrl_m4_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_db_footprintDB-plants.html
;	dyads_test_vs_ctrl_m4_vs_ref  	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_ref.tab
;	dyads_test_vs_ctrl_m4_vs_ref_html	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_ref.html
;	dyads_test_vs_ctrl_m5_logo    	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_logo.png
;	dyads_test_vs_ctrl_m5_logo_rc 	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_logo_rc.png
;	dyads_test_vs_ctrl_m5_pssm_enrichment	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_scan_mkv1_enrichment.tab
;	dyads_test_vs_ctrl_m5_pssm_enrichment_png	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_scan_mkv1_enrichment.png
;	dyads_test_vs_ctrl_m5_pssm_site_distrib	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_site_distrib.tab
;	dyads_test_vs_ctrl_m5_pssm_site_distrib_graph	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_site_distrib.png
;	dyads_test_vs_ctrl_m5_pssm_sites	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_sites.tab
;	dyads_test_vs_ctrl_m5_pssm_sites_per_peak	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_sites_per_peak.tab
;	dyads_test_vs_ctrl_m5_pssm_sites_per_peak_graph	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_sites_per_peak.png
;	dyads_test_vs_ctrl_m5_tab     	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tab
;	dyads_test_vs_ctrl_m5_tf      	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tf
;	dyads_test_vs_ctrl_m5_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_vs_db_footprintDB-plants.tab
;	dyads_test_vs_ctrl_m5_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_vs_db_footprintDB-plants.html
;	dyads_test_vs_ctrl_m5_vs_ref  	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_vs_ref.tab
;	dyads_test_vs_ctrl_m5_vs_ref_html	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_vs_ref.html
;	dyads_test_vs_ctrl_m6_logo    	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_logo.png
;	dyads_test_vs_ctrl_m6_logo_rc 	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_logo_rc.png
;	dyads_test_vs_ctrl_m6_pssm_enrichment	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_scan_mkv1_enrichment.tab
;	dyads_test_vs_ctrl_m6_pssm_enrichment_png	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_scan_mkv1_enrichment.png
;	dyads_test_vs_ctrl_m6_pssm_site_distrib	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_site_distrib.tab
;	dyads_test_vs_ctrl_m6_pssm_site_distrib_graph	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_site_distrib.png
;	dyads_test_vs_ctrl_m6_pssm_sites	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_sites.tab
;	dyads_test_vs_ctrl_m6_pssm_sites_per_peak	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_sites_per_peak.tab
;	dyads_test_vs_ctrl_m6_pssm_sites_per_peak_graph	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_sites_per_peak.png
;	dyads_test_vs_ctrl_m6_tab     	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6.tab
;	dyads_test_vs_ctrl_m6_tf      	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6.tf
;	dyads_test_vs_ctrl_m6_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_vs_db_footprintDB-plants.tab
;	dyads_test_vs_ctrl_m6_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_vs_db_footprintDB-plants.html
;	dyads_test_vs_ctrl_m6_vs_ref  	peaks-rm-orig/results/discovered_motifs/dyads_test_vs_ctrl_m6/peaks_dyads_test_vs_ctrl_m6_vs_ref.tab
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;	oligos_6-8nt_m6_vs_db_footprintDB-plants	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_vs_db_footprintDB-plants.tab
;	oligos_6-8nt_m6_vs_db_footprintDB-plants_html	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_vs_db_footprintDB-plants.html
;	oligos_6-8nt_m6_vs_ref        	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_vs_ref.tab
;	oligos_6-8nt_m6_vs_ref_html   	peaks-rm-orig/results/discovered_motifs/oligos_6-8nt_m6/peaks_oligos_6-8nt_m6_vs_ref.html
;	oligos_6-8nt_pssm_counts      	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices.txt
;	oligos_6-8nt_pssm_logo1       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m1.png
;	oligos_6-8nt_pssm_logo2       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m2.png
;	oligos_6-8nt_pssm_logo3       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m3.png
;	oligos_6-8nt_pssm_logo4       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m4.png
;	oligos_6-8nt_pssm_logo5       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m5.png
;	oligos_6-8nt_pssm_logo6       	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m6.png
;	oligos_6-8nt_pssm_logo_rc1    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m1_rc.png
;	oligos_6-8nt_pssm_logo_rc2    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m2_rc.png
;	oligos_6-8nt_pssm_logo_rc3    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m3_rc.png
;	oligos_6-8nt_pssm_logo_rc4    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m4_rc.png
;	oligos_6-8nt_pssm_logo_rc5    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m5_rc.png
;	oligos_6-8nt_pssm_logo_rc6    	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices_logo_m6_rc.png
;	oligos_6-8nt_pssm_sig         	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_sig_matrices.tf
;	oligos_6-8nt_pssm_tf          	peaks-rm-orig/results/oligos_6-8nt/peaks_oligos-2str-noov_6-8nt_mvk-2_-2_pssm_count_matrices.tf
;	oligos_6nt_test_vs_ctrl       	peaks-rm-orig/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab
;	oligos_6nt_test_vs_ctrl_bg_file	peaks-rm-orig/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab
;	oligos_7nt_test_vs_ctrl       	peaks-rm-orig/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab
;	oligos_7nt_test_vs_ctrl_bg_file	peaks-rm-orig/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab
;	oligos_8nt_test_vs_ctrl       	peaks-rm-orig/results/oligos_8nt_test_vs_ctrl/peaks_oligos-2str-noov_8nt_test_vs_ctrl.tab
;	oligos_8nt_test_vs_ctrl_bg_file	peaks-rm-orig/results/oligos_8nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_8nt-2str-noov.tab
;	small_summary                 	peaks-rm-orig/peaks_small_summary.html
;	small_summary_txt             	peaks-rm-orig/reports/peaks_small_summary.txt
;	synthesis                     	peaks-rm-orig/peaks_synthesis.html
;	test_converted                	peaks-rm-orig/data/sequences/peaks_test.fasta
;	test_purged                   	peaks-rm-orig/data/sequences/peaks_test_purged_ml40_mis3.fasta
;	test_seqlen                   	peaks-rm-orig/data/sequences/peaks_test_seqlen.tab
;	test_seqlen_distrib           	peaks-rm-orig/data/sequences/peaks_test_seqlen_distrib.tab
;	test_seqlen_distrib_graph     	peaks-rm-orig/data/sequences/peaks_test_seqlen_distrib.png
;	timelog                       	peaks-rm-orig/reports/peaks_timelog.txt
;	timelog_html                  	peaks-rm-orig/reports/peaks_timelog.html
;	timetable                     	peaks-rm-orig/reports/peaks_timetable.txt

; 2023-05-30.162705
$RSAT/perl-scripts/text-to-html -i peaks-rm-orig/reports/peaks_small_summary.txt -no_sort  -o peaks-rm-orig/peaks_small_summary.html