; 2025-01-04.192524
peak-motifs  -v 1 -title control -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh



; 2025-01-04.192524
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/images_html


; 2025-01-04.192524
$RSAT/perl-scripts/convert-seq -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifspeak_seq -from fasta -to fasta -mask non-dna | $RSAT/perl-scripts/sub-sequence -origin center -from -500 -to 499 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta


; 2025-01-04.192524
$RSAT/perl-scripts/purge-sequence -dna -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -ml 40 -mis 3 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta


; 2025-01-04.192528
$RSAT/perl-scripts/sequence-lengths -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_seqlen.tab -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_seqlen_distrib.tab


; 2025-01-04.192528
$RSAT/perl-scripts/XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; control' -xsize 700 -xcol 3 -xleg1 'Peak length' -ysize 250 -ycol 4 -yleg1 'Number of peaks' -xmin 0 -ymin 0 -xgstep2 20 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_seqlen_distrib.tab -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_seqlen_distrib.png


; 2025-01-04.192528
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab_time.txt $RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -l 1 -1str -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab


; 2025-01-04.192528
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_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 $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png


; 2025-01-04.192528
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab_time.txt $RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -l 2 -1str -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab


; 2025-01-04.192529
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_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 $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png


; 2025-01-04.192529
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab_time.txt $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_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 'control' -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab


; 2025-01-04.192537
grep -v ";" $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_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; control' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png


; 2025-01-04.192537
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab_time.txt $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_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 'control' -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab


; 2025-01-04.192547
grep -v ";" $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_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; control' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png


; 2025-01-04.192548
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab_time.txt $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_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 -markov 4 -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab


; 2025-01-04.192549
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_6nt_mkv4 -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm


; 2025-01-04.192556
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5.tab_time.txt $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_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 -markov 5 -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5.tab


; 2025-01-04.192558
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5.tab -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_7nt_mkv5 -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5_pssm


; 2025-01-04.192607
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab_time.txt $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort  -return chi,sig,rank,distrib,index -max_graphs 100 -2str -noov -seqtype dna -l 6 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title 'control' -origin center -offset 0 -max_graphs 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab


; 2025-01-04.192620
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix positions_6nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm


; 2025-01-04.192627
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab_time.txt $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort  -return chi,sig,rank,distrib,index -max_graphs 100 -2str -noov -seqtype dna -l 7 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title 'control' -origin center -offset 0 -max_graphs 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab


; 2025-01-04.192646
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix positions_7nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm


; 2025-01-04.192651
rm -f $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_discovered.tf


; 2025-01-04.192652
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tab


; 2025-01-04.192652
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tab


; 2025-01-04.192652
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tab


; 2025-01-04.192652
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tab


; 2025-01-04.192652
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.tab


; 2025-01-04.192653
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tab


; 2025-01-04.192653
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tab


; 2025-01-04.192653
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tab


; 2025-01-04.192653
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tab


; 2025-01-04.192653
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tab


; 2025-01-04.192653
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tab


; 2025-01-04.192654
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tab


; 2025-01-04.192654
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tab


; 2025-01-04.192654
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.tab


; 2025-01-04.192654
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.tab


; 2025-01-04.192654
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tab


; 2025-01-04.192655
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tab


; 2025-01-04.192655
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tab


; 2025-01-04.192655
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tab


; 2025-01-04.192655
$RSAT/perl-scripts/compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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 $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab; $RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_disco_compa.html


; 2025-01-04.192710
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml


; 2025-01-04.192710
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab


; 2025-01-04.192711
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.tab


; 2025-01-04.192711
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv4_m1' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.png


; 2025-01-04.192712
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.tab


; 2025-01-04.192712
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv4_m1' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.png


; 2025-01-04.192712
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab


; 2025-01-04.192713
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_site_distrib.tab


; 2025-01-04.192713
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv4_m2' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_site_distrib.png


; 2025-01-04.192713
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_per_peak.tab


; 2025-01-04.192713
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv4_m2' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_per_peak.png


; 2025-01-04.192713
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab


; 2025-01-04.192714
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_site_distrib.tab


; 2025-01-04.192715
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv4_m3' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_site_distrib.png


; 2025-01-04.192715
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_per_peak.tab


; 2025-01-04.192715
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv4_m3' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_per_peak.png


; 2025-01-04.192715
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab


; 2025-01-04.192716
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_site_distrib.tab


; 2025-01-04.192716
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv4_m4' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_site_distrib.png


; 2025-01-04.192716
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites_per_peak.tab


; 2025-01-04.192716
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv4_m4' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites_per_peak.png


; 2025-01-04.192716
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab


; 2025-01-04.192717
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_site_distrib.tab


; 2025-01-04.192718
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv4_m5' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_site_distrib.png


; 2025-01-04.192718
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites_per_peak.tab


; 2025-01-04.192718
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv4_m5' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites_per_peak.png


; 2025-01-04.192718
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab


; 2025-01-04.192719
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.tab


; 2025-01-04.192719
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_6nt_m1' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.png


; 2025-01-04.192719
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.tab


; 2025-01-04.192720
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_6nt_m1' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.png


; 2025-01-04.192720
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab


; 2025-01-04.192721
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.tab


; 2025-01-04.192721
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_6nt_m2' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.png


; 2025-01-04.192721
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.tab


; 2025-01-04.192721
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_6nt_m2' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.png


; 2025-01-04.192721
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab


; 2025-01-04.192723
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.tab


; 2025-01-04.192723
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_6nt_m3' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.png


; 2025-01-04.192723
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.tab


; 2025-01-04.192723
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_6nt_m3' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.png


; 2025-01-04.192723
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab


; 2025-01-04.192724
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_site_distrib.tab


; 2025-01-04.192724
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_6nt_m4' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_site_distrib.png


; 2025-01-04.192724
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_per_peak.tab


; 2025-01-04.192725
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_6nt_m4' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_per_peak.png


; 2025-01-04.192725
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab


; 2025-01-04.192726
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_site_distrib.tab


; 2025-01-04.192726
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_6nt_m5' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_site_distrib.png


; 2025-01-04.192726
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_per_peak.tab


; 2025-01-04.192726
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_6nt_m5' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_per_peak.png


; 2025-01-04.192726
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab


; 2025-01-04.192727
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_site_distrib.tab


; 2025-01-04.192727
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv5_m1' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_site_distrib.png


; 2025-01-04.192728
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_per_peak.tab


; 2025-01-04.192728
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv5_m1' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_per_peak.png


; 2025-01-04.192728
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab


; 2025-01-04.192729
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_site_distrib.tab


; 2025-01-04.192729
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv5_m2' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_site_distrib.png


; 2025-01-04.192729
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_per_peak.tab


; 2025-01-04.192729
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv5_m2' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_per_peak.png


; 2025-01-04.192729
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab


; 2025-01-04.192730
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_site_distrib.tab


; 2025-01-04.192730
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv5_m3' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_site_distrib.png


; 2025-01-04.192731
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_per_peak.tab


; 2025-01-04.192731
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv5_m3' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_per_peak.png


; 2025-01-04.192731
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab


; 2025-01-04.192732
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_site_distrib.tab


; 2025-01-04.192732
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv5_m4' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_site_distrib.png


; 2025-01-04.192732
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites_per_peak.tab


; 2025-01-04.192732
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv5_m4' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites_per_peak.png


; 2025-01-04.192733
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab


; 2025-01-04.192734
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_site_distrib.tab


; 2025-01-04.192734
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv5_m5' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_site_distrib.png


; 2025-01-04.192734
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites_per_peak.tab


; 2025-01-04.192734
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv5_m5' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites_per_peak.png


; 2025-01-04.192734
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab


; 2025-01-04.192735
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.tab


; 2025-01-04.192735
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_7nt_m1' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.png


; 2025-01-04.192736
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.tab


; 2025-01-04.192736
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_7nt_m1' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.png


; 2025-01-04.192736
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab


; 2025-01-04.192737
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.tab


; 2025-01-04.192737
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_7nt_m2' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.png


; 2025-01-04.192737
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.tab


; 2025-01-04.192737
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_7nt_m2' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.png


; 2025-01-04.192737
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab


; 2025-01-04.192738
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.tab


; 2025-01-04.192738
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_7nt_m3' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.png


; 2025-01-04.192739
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.tab


; 2025-01-04.192739
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_7nt_m3' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.png


; 2025-01-04.192739
time -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab


; 2025-01-04.192740
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_site_distrib.tab


; 2025-01-04.192740
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_7nt_m4' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_site_distrib.png


; 2025-01-04.192740
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_per_peak.tab


; 2025-01-04.192740
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_7nt_m4' -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_per_peak.png


; 2025-01-04.192740
cat $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab > $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/sites/peak-motifs_all_motifs_seqcoord.tab


; 2025-01-04.192741
$RSAT/perl-scripts/text-to-html -font variable -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_timelog.txt -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_timelog.html

; peak-motifs  -v 1 -title control -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh
; Program version       	1.256
; Parameter values
;	seq_format            	fasta
;	img_format            	png
;	ref_motifs_format     	transfac
;	purge_match_length    	40
;	purge_mismatches      	3
;	origin                	center
;	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         	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
;	test_seq              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifspeak_seq
; Directories
;	output                        	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/
;	oligos_6nt_mkv4_m1            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/
;	oligos_6nt_mkv4_m2            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/
;	oligos_6nt_mkv4_m3            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/
;	oligos_6nt_mkv4_m4            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/
;	oligos_6nt_mkv4_m5            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/
;	positions_6nt_m1              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/
;	positions_6nt_m2              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/
;	positions_6nt_m3              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/
;	positions_6nt_m4              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/
;	positions_6nt_m5              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/
;	oligos_7nt_mkv5_m1            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/
;	oligos_7nt_mkv5_m2            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/
;	oligos_7nt_mkv5_m3            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/
;	oligos_7nt_mkv5_m4            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/
;	oligos_7nt_mkv5_m5            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/
;	positions_7nt_m1              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/
;	positions_7nt_m2              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/
;	positions_7nt_m3              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/
;	positions_7nt_m4              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/
; Output files
;	1nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_test_transitions          	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab
;	2nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab
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;	small_summary_txt             	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_small_summary.txt
;	synthesis                     	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifs_synthesis.html
;	test_converted                	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta
;	test_purged                   	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta
;	test_seqlen                   	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_seqlen.tab
;	test_seqlen_distrib           	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_seqlen_distrib.tab
;	test_seqlen_distrib_graph     	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_seqlen_distrib.png
;	timelog                       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_timelog.txt
;	timelog_html                  	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_timelog.html
;	timetable                     	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_timetable.txt

; 2025-01-04.192741
(cd $RSAT/public_html/tmp/www-data/2025/01/04 ;  zip -ryq peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifs_archive.zip peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh -x peak-motifs_archive.zip)


; 2025-01-04.192743
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/images_html

; peak-motifs  -v 1 -title control -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh
; Program version       	1.256
; Parameter values
;	seq_format            	fasta
;	img_format            	png
;	ref_motifs_format     	transfac
;	purge_match_length    	40
;	purge_mismatches      	3
;	origin                	center
;	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         	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
;	test_seq              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifspeak_seq
; Directories
;	output                        	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/
;	oligos_6nt_mkv4_m1            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/
;	oligos_6nt_mkv4_m2            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m2/
;	oligos_6nt_mkv4_m3            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m3/
;	oligos_6nt_mkv4_m4            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m4/
;	oligos_6nt_mkv4_m5            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m5/
;	positions_6nt_m1              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m1/
;	positions_6nt_m2              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m2/
;	positions_6nt_m3              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m3/
;	positions_6nt_m4              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m4/
;	positions_6nt_m5              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_6nt_m5/
;	oligos_7nt_mkv5_m1            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m1/
;	oligos_7nt_mkv5_m2            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m2/
;	oligos_7nt_mkv5_m3            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m3/
;	oligos_7nt_mkv5_m4            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m4/
;	oligos_7nt_mkv5_m5            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_7nt_mkv5_m5/
;	positions_7nt_m1              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m1/
;	positions_7nt_m2              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m2/
;	positions_7nt_m3              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/
;	positions_7nt_m4              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/
; Output files
;	1nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_test_transitions          	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab
;	2nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_test_transitions          	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab
;	archive                       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifs_archive.zip
;	links                         	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_links.html
;	log                           	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_log.txt
;	merged_sites                  	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/sites/peak-motifs_all_motifs_seqcoord.tab
;	merged_sites_bed              	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/sites/peak-motifs_all_motifs_seqcoord.bed
;	merged_words                  	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/merged_words/peak-motifs_merged_words.tab
;	merged_words_heatmap          	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/merged_words/peak-motifs_merged_words_heatmap.png
;	merged_words_html             	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/merged_words/peak-motifs_merged_words.html
;	motifs_disco_clusters         	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_discovered_clusters
;	motifs_disco_clusters_html    	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_discovered_clusters_SUMMARY.html
;	motifs_disco_compa            	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
;	motifs_disco_compa_alignments_1ton	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.tab
;	motifs_disco_compa_alignments_1ton_html	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.html
;	motifs_disco_compa_gml        	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml
;	motifs_disco_compa_html       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_disco_compa.html
;	motifs_discovered             	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_discovered.tf
;	motifs_discovered_table       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/peak-motifs_motifs_discovered_table.tab
;	oligos_6nt_mkv4               	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab
;	oligos_6nt_mkv4_2pssm         	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_log.txt
;	oligos_6nt_mkv4_asmb          	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm.asmb
;	oligos_6nt_mkv4_m1_logo       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_logo.png
;	oligos_6nt_mkv4_m1_logo_rc    	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_logo_rc.png
;	oligos_6nt_mkv4_m1_pssm_enrichment	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv1_enrichment.tab
;	oligos_6nt_mkv4_m1_pssm_enrichment_png	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv1_enrichment.png
;	oligos_6nt_mkv4_m1_pssm_site_distrib	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.tab
;	oligos_6nt_mkv4_m1_pssm_site_distrib_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.png
;	oligos_6nt_mkv4_m1_pssm_sites 	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab
;	oligos_6nt_mkv4_m1_pssm_sites_per_peak	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.tab
;	oligos_6nt_mkv4_m1_pssm_sites_per_peak_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.png
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;	positions_7nt_m3_logo_rc      	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_logo_rc.png
;	positions_7nt_m3_pssm_enrichment	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv1_enrichment.tab
;	positions_7nt_m3_pssm_enrichment_png	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv1_enrichment.png
;	positions_7nt_m3_pssm_site_distrib	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.tab
;	positions_7nt_m3_pssm_site_distrib_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.png
;	positions_7nt_m3_pssm_sites   	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab
;	positions_7nt_m3_pssm_sites_per_peak	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.tab
;	positions_7nt_m3_pssm_sites_per_peak_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.png
;	positions_7nt_m3_tab          	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tab
;	positions_7nt_m3_tf           	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf
;	positions_7nt_m3_vs_ref       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_ref.tab
;	positions_7nt_m3_vs_ref_html  	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_ref.html
;	positions_7nt_m4_logo         	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_logo.png
;	positions_7nt_m4_logo_rc      	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_logo_rc.png
;	positions_7nt_m4_pssm_enrichment	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_scan_mkv1_enrichment.tab
;	positions_7nt_m4_pssm_enrichment_png	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_scan_mkv1_enrichment.png
;	positions_7nt_m4_pssm_site_distrib	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_site_distrib.tab
;	positions_7nt_m4_pssm_site_distrib_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_site_distrib.png
;	positions_7nt_m4_pssm_sites   	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab
;	positions_7nt_m4_pssm_sites_per_peak	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_per_peak.tab
;	positions_7nt_m4_pssm_sites_per_peak_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_per_peak.png
;	positions_7nt_m4_tab          	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tab
;	positions_7nt_m4_tf           	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf
;	positions_7nt_m4_vs_ref       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_ref.tab
;	positions_7nt_m4_vs_ref_html  	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_ref.html
;	positions_7nt_pssm_counts     	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.txt
;	positions_7nt_pssm_logo1      	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m1.png
;	positions_7nt_pssm_logo2      	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m2.png
;	positions_7nt_pssm_logo3      	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m3.png
;	positions_7nt_pssm_logo4      	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m4.png
;	positions_7nt_pssm_logo5      	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m5.png
;	positions_7nt_pssm_logo_rc1   	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m1_rc.png
;	positions_7nt_pssm_logo_rc2   	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m2_rc.png
;	positions_7nt_pssm_logo_rc3   	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m3_rc.png
;	positions_7nt_pssm_logo_rc4   	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m4_rc.png
;	positions_7nt_pssm_logo_rc5   	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m5_rc.png
;	positions_7nt_pssm_sig        	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices.tf
;	positions_7nt_pssm_tf         	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf
;	small_summary                 	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifs_small_summary.html
;	small_summary_txt             	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_small_summary.txt
;	synthesis                     	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifs_synthesis.html
;	test_converted                	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000.fasta
;	test_purged                   	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta
;	test_seqlen                   	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_seqlen.tab
;	test_seqlen_distrib           	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_seqlen_distrib.tab
;	test_seqlen_distrib_graph     	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/data/sequences/peak-motifs_test_seqlen_distrib.png
;	timelog                       	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_timelog.txt
;	timelog_html                  	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_timelog.html
;	timetable                     	/var/www/html/rsat/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_timetable.txt

; 2025-01-04.192743
(cd $RSAT/public_html/tmp/www-data/2025/01/04 ;  zip -ryq peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifs_archive.zip peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifs_synthesis.html -x peak-motifs_archive.zip)


; 2025-01-04.192743
$RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/reports/peak-motifs_small_summary.txt -no_sort  -o $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifs_small_summary.html


; 2025-01-04.192743
(cd $RSAT/public_html/tmp/www-data/2025/01/04 ;  zip -ryq peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifs_archive.zip peak-motifs.2025-01-04.192524_2025-01-04.192524_fvZzZh/peak-motifs_small_summary.html -x peak-motifs_archive.zip)

; Host name	rsat
; Job started	2025-01-04.192524
; Job done	2025-01-04.192743
; Seconds	0.71
;	user	0.71
;	system	0.61
;	cuser	132.18
;	csystem	9.78