; 2015-11-03.065541
peak-motifs  -v 1 -title fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks_1slk_20151103_065518 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db jaspar_core_vertebrates tf $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx



; 2015-11-03.065541
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/images_html


; 2015-11-03.065541
$RSAT/perl-scripts/convert-seq -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta


; 2015-11-03.065542
$RSAT/perl-scripts/purge-sequence -dna -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -ml 40 -mis 3 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta


; 2015-11-03.065543
$RSAT/perl-scripts/sequence-lengths -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_seqlen.tab -ci 20 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_seqlen_distrib.tab


; 2015-11-03.065543
$RSAT/perl-scripts/XYgraph -lines -pointsize 0 -legend -format png -title 'Sequence lengths; fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks_1slk_20151103_065518' -ysize 200 -ycol 4 -yleg1 'Number of peaks' -xsize 800 -xcol 3 -xleg1 'Peak length' -xmin 0 -ymin 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_seqlen_distrib.tab -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_seqlen_distrib.png


; 2015-11-03.065544
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -l 1 -1str > $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab


; 2015-11-03.065544
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1  -out_format png -col_width 50 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png


; 2015-11-03.065545
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -l 2 -1str > $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab


; 2015-11-03.065545
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1  -out_format png -col_width 50 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png


; 2015-11-03.065546
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 'fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks_1slk_20151103_065518' -origin center -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab


; 2015-11-03.065551
grep -v ";" $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -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; fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks_1slk_20151103_065518' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300  -ymin 0 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png


; 2015-11-03.065551
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 'fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks_1slk_20151103_065518' -origin center -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab


; 2015-11-03.065602
grep -v ";" $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -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; fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks_1slk_20151103_065518' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300  -ymin 0 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png


; 2015-11-03.065603
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.tab_time.txt $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 3 -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.tab


; 2015-11-03.065604
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.tab -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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_mkv3 -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm


; 2015-11-03.065618
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4.tab_time.txt $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 4 -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4.tab


; 2015-11-03.065621
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4.tab -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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_mkv4 -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4_pssm


; 2015-11-03.065636
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 'fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks_1slk_20151103_065518' -origin center -max_graphs 20 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab


; 2015-11-03.065643
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm


; 2015-11-03.065701
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 'fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks_1slk_20151103_065518' -origin center -max_graphs 20 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab


; 2015-11-03.065714
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm


; 2015-11-03.065734
rm -f $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_discovered.tf


; 2015-11-03.065734
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1.tab


; 2015-11-03.065735
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2.tab


; 2015-11-03.065735
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3.tab


; 2015-11-03.065735
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4.tab


; 2015-11-03.065736
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5.tab


; 2015-11-03.065736
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tab


; 2015-11-03.065736
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tab


; 2015-11-03.065737
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tab


; 2015-11-03.065737
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tab


; 2015-11-03.065738
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tab


; 2015-11-03.065738
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1.tab


; 2015-11-03.065738
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2.tab


; 2015-11-03.065739
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3.tab


; 2015-11-03.065739
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4.tab


; 2015-11-03.065739
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5.tab


; 2015-11-03.065740
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tab


; 2015-11-03.065740
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tab


; 2015-11-03.065741
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tab


; 2015-11-03.065741
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tab


; 2015-11-03.065741
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tab


; 2015-11-03.065742
$RSAT/perl-scripts/compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab; $RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_disco_compa.html


; 2015-11-03.065830
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml


; 2015-11-03.065832
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_vs_db_jaspar_core_vertebrates


; 2015-11-03.065844
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_jaspar_core_vertebrates


; 2015-11-03.065853
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_jaspar_core_vertebrates


; 2015-11-03.065905
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_vs_db_jaspar_core_vertebrates


; 2015-11-03.065908
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_vs_db_jaspar_core_vertebrates


; 2015-11-03.065911
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_jaspar_core_vertebrates


; 2015-11-03.065924
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_jaspar_core_vertebrates


; 2015-11-03.065938
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_jaspar_core_vertebrates


; 2015-11-03.065951
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_vs_db_jaspar_core_vertebrates


; 2015-11-03.070004
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_vs_db_jaspar_core_vertebrates


; 2015-11-03.070016
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_vs_db_jaspar_core_vertebrates


; 2015-11-03.070028
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_vs_db_jaspar_core_vertebrates


; 2015-11-03.070040
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_vs_db_jaspar_core_vertebrates


; 2015-11-03.070051
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_vs_db_jaspar_core_vertebrates


; 2015-11-03.070101
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_vs_db_jaspar_core_vertebrates


; 2015-11-03.070112
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates


; 2015-11-03.070124
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_jaspar_core_vertebrates


; 2015-11-03.070137
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_vertebrates


; 2015-11-03.070141
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_db_jaspar_core_vertebrates


; 2015-11-03.070153
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_jaspar_core_vertebrates


; 2015-11-03.070207
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab_time.txt $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab


; 2015-11-03.070510
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.gml


; 2015-11-03.070512
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_sites.tab


; 2015-11-03.070513
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_site_distrib.tab


; 2015-11-03.070513
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv3_m1' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_site_distrib.png


; 2015-11-03.070514
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_sites_per_peak.tab


; 2015-11-03.070514
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv3_m1' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_sites_per_peak.png


; 2015-11-03.070514
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_scan_mkv1_enrichment.tab


; 2015-11-03.070518
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_scan_mkv1_enrichment.png


; 2015-11-03.070518
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_sites.tab


; 2015-11-03.070519
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_site_distrib.tab


; 2015-11-03.070520
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv3_m2' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_site_distrib.png


; 2015-11-03.070520
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_sites_per_peak.tab


; 2015-11-03.070520
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv3_m2' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_sites_per_peak.png


; 2015-11-03.070521
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_scan_mkv1_enrichment.tab


; 2015-11-03.070523
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_scan_mkv1_enrichment.png


; 2015-11-03.070523
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_sites.tab


; 2015-11-03.070524
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_site_distrib.tab


; 2015-11-03.070524
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv3_m3' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_site_distrib.png


; 2015-11-03.070525
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_sites_per_peak.tab


; 2015-11-03.070525
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv3_m3' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_sites_per_peak.png


; 2015-11-03.070525
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_scan_mkv1_enrichment.tab


; 2015-11-03.070528
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_scan_mkv1_enrichment.png


; 2015-11-03.070528
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_sites.tab


; 2015-11-03.070529
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_site_distrib.tab


; 2015-11-03.070530
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv3_m4' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_site_distrib.png


; 2015-11-03.070530
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_sites_per_peak.tab


; 2015-11-03.070530
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv3_m4' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_sites_per_peak.png


; 2015-11-03.070531
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_scan_mkv1_enrichment.tab


; 2015-11-03.070533
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_scan_mkv1_enrichment.png


; 2015-11-03.070533
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_sites.tab


; 2015-11-03.070534
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_site_distrib.tab


; 2015-11-03.070535
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv3_m5' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_site_distrib.png


; 2015-11-03.070535
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_sites_per_peak.tab


; 2015-11-03.070535
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv3_m5' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_sites_per_peak.png


; 2015-11-03.070536
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_scan_mkv1_enrichment.tab


; 2015-11-03.070538
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_scan_mkv1_enrichment.png


; 2015-11-03.070538
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab


; 2015-11-03.070539
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.tab


; 2015-11-03.070540
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m1' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.png


; 2015-11-03.070540
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.tab


; 2015-11-03.070540
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m1' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.png


; 2015-11-03.070541
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv1_enrichment.tab


; 2015-11-03.070545
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv1_enrichment.png


; 2015-11-03.070545
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab


; 2015-11-03.070546
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.tab


; 2015-11-03.070547
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m2' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.png


; 2015-11-03.070547
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.tab


; 2015-11-03.070547
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m2' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.png


; 2015-11-03.070548
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv1_enrichment.tab


; 2015-11-03.070552
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv1_enrichment.png


; 2015-11-03.070552
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab


; 2015-11-03.070554
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.tab


; 2015-11-03.070554
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m3' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.png


; 2015-11-03.070554
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.tab


; 2015-11-03.070555
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m3' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.png


; 2015-11-03.070555
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv1_enrichment.tab


; 2015-11-03.070559
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv1_enrichment.png


; 2015-11-03.070559
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab


; 2015-11-03.070601
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_site_distrib.tab


; 2015-11-03.070601
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m4' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_site_distrib.png


; 2015-11-03.070601
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_per_peak.tab


; 2015-11-03.070602
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m4' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites_per_peak.png


; 2015-11-03.070602
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_scan_mkv1_enrichment.tab


; 2015-11-03.070606
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_scan_mkv1_enrichment.png


; 2015-11-03.070606
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab


; 2015-11-03.070608
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_site_distrib.tab


; 2015-11-03.070608
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m5' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_site_distrib.png


; 2015-11-03.070608
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_per_peak.tab


; 2015-11-03.070609
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m5' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites_per_peak.png


; 2015-11-03.070609
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_scan_mkv1_enrichment.tab


; 2015-11-03.070612
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_scan_mkv1_enrichment.png


; 2015-11-03.070613
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_sites.tab


; 2015-11-03.070614
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_site_distrib.tab


; 2015-11-03.070614
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv4_m1' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_site_distrib.png


; 2015-11-03.070615
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_sites_per_peak.tab


; 2015-11-03.070615
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv4_m1' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_sites_per_peak.png


; 2015-11-03.070615
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_scan_mkv1_enrichment.tab


; 2015-11-03.070619
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_scan_mkv1_enrichment.png


; 2015-11-03.070619
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_sites.tab


; 2015-11-03.070620
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_site_distrib.tab


; 2015-11-03.070621
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv4_m2' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_site_distrib.png


; 2015-11-03.070621
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_sites_per_peak.tab


; 2015-11-03.070621
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv4_m2' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_sites_per_peak.png


; 2015-11-03.070622
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_scan_mkv1_enrichment.tab


; 2015-11-03.070625
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_scan_mkv1_enrichment.png


; 2015-11-03.070625
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_sites.tab


; 2015-11-03.070626
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_site_distrib.tab


; 2015-11-03.070627
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv4_m3' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_site_distrib.png


; 2015-11-03.070627
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_sites_per_peak.tab


; 2015-11-03.070627
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv4_m3' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_sites_per_peak.png


; 2015-11-03.070628
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_scan_mkv1_enrichment.tab


; 2015-11-03.070631
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_scan_mkv1_enrichment.png


; 2015-11-03.070631
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_sites.tab


; 2015-11-03.070632
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_site_distrib.tab


; 2015-11-03.070632
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv4_m4' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_site_distrib.png


; 2015-11-03.070633
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_sites_per_peak.tab


; 2015-11-03.070633
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv4_m4' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_sites_per_peak.png


; 2015-11-03.070633
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_scan_mkv1_enrichment.tab


; 2015-11-03.070636
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_scan_mkv1_enrichment.png


; 2015-11-03.070636
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_sites.tab


; 2015-11-03.070637
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_site_distrib.tab


; 2015-11-03.070638
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv4_m5' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_site_distrib.png


; 2015-11-03.070638
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_sites_per_peak.tab


; 2015-11-03.070638
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv4_m5' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_sites_per_peak.png


; 2015-11-03.070639
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_scan_mkv1_enrichment.tab


; 2015-11-03.070641
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_scan_mkv1_enrichment.png


; 2015-11-03.070642
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab


; 2015-11-03.070643
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.tab


; 2015-11-03.070643
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m1' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.png


; 2015-11-03.070644
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.tab


; 2015-11-03.070644
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m1' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.png


; 2015-11-03.070644
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv1_enrichment.tab


; 2015-11-03.070648
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv1_enrichment.png


; 2015-11-03.070649
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab


; 2015-11-03.070650
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.tab


; 2015-11-03.070650
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m2' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.png


; 2015-11-03.070651
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.tab


; 2015-11-03.070651
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m2' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.png


; 2015-11-03.070651
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv1_enrichment.tab


; 2015-11-03.070656
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv1_enrichment.png


; 2015-11-03.070656
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab


; 2015-11-03.070657
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.tab


; 2015-11-03.070658
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m3' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.png


; 2015-11-03.070658
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.tab


; 2015-11-03.070658
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m3' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.png


; 2015-11-03.070659
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv1_enrichment.tab


; 2015-11-03.070703
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv1_enrichment.png


; 2015-11-03.070703
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab


; 2015-11-03.070704
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_site_distrib.tab


; 2015-11-03.070705
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m4' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_site_distrib.png


; 2015-11-03.070705
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_per_peak.tab


; 2015-11-03.070705
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m4' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites_per_peak.png


; 2015-11-03.070706
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_scan_mkv1_enrichment.tab


; 2015-11-03.070710
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_scan_mkv1_enrichment.png


; 2015-11-03.070710
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 -return sites -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab


; 2015-11-03.070711
grep -v '^;' $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_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/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_site_distrib.tab


; 2015-11-03.070712
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m5' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_site_distrib.png


; 2015-11-03.070712
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites_per_peak.tab


; 2015-11-03.070712
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m5' -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites_per_peak.png


; 2015-11-03.070713
time -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_scan_mkv1_enrichment.tab_time.txt $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_scan_mkv1_enrichment.tab


; 2015-11-03.070717
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_scan_mkv1_enrichment.png


; 2015-11-03.070717
cat $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_sites.tab $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab > $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/sites/peak-motifs_all_motifs_seqcoord.tab


; 2015-11-03.070733
$RSAT/perl-scripts/text-to-html -font variable -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/reports/peak-motifs_timelog.txt -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/reports/peak-motifs_timelog.html

; peak-motifs  -v 1 -title fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks_1slk_20151103_065518 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db jaspar_core_vertebrates tf $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx
; 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
;	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         	-3
;	oligo_max_mkv         	-3
;	positions_max_graphs  	20
;	asmb_toppat           	100
;	max_asmb_width        	20
;	matrix_nmotifs        	5
; Input files
;	motif_db_jaspar_core_vertebrates	/workspace/rsat/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf
;	test_seq              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/peak-motifspeak_seq
; Directories
;	output                        	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/
;	oligos_6nt_mkv3_m1            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m1/
;	oligos_6nt_mkv3_m2            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/
;	oligos_6nt_mkv3_m3            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m3/
;	oligos_6nt_mkv3_m4            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m4/
;	oligos_6nt_mkv3_m5            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m5/
;	positions_6nt_m1              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m1/
;	positions_6nt_m2              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m2/
;	positions_6nt_m3              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m3/
;	positions_6nt_m4              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m4/
;	positions_6nt_m5              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_6nt_m5/
;	oligos_7nt_mkv4_m1            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/
;	oligos_7nt_mkv4_m2            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m2/
;	oligos_7nt_mkv4_m3            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m3/
;	oligos_7nt_mkv4_m4            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m4/
;	oligos_7nt_mkv4_m5            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m5/
;	positions_7nt_m1              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/
;	positions_7nt_m2              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m2/
;	positions_7nt_m3              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m3/
;	positions_7nt_m4              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/
;	positions_7nt_m5              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/
; Output files
;	1nt_test_freq                 	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_test_transitions          	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab
;	2nt_test_freq                 	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_test_transitions          	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab
;	archive                       	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/peak-motifs_archive.zip
;	links                         	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/reports/peak-motifs_links.html
;	log                           	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/reports/peak-motifs_log.txt
;	merged_sites                  	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/sites/peak-motifs_all_motifs_seqcoord.tab
;	merged_sites_bed              	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/sites/peak-motifs_all_motifs_seqcoord.bed
;	merged_words                  	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/merged_words/peak-motifs_merged_words.tab
;	merged_words_heatmap          	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/merged_words/peak-motifs_merged_words_heatmap.png
;	merged_words_html             	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/merged_words/peak-motifs_merged_words.html
;	motifs_disco_clusters         	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_discovered_clusters
;	motifs_disco_clusters_html    	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_discovered_clusters_SUMMARY.html
;	motifs_disco_compa            	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
;	motifs_disco_compa_alignments_1ton	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.tab
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;	positions_7nt_m4_vs_db_jaspar_core_vertebrates	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_db_jaspar_core_vertebrates.tab
;	positions_7nt_m4_vs_db_jaspar_core_vertebrates_html	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_db_jaspar_core_vertebrates.html
;	positions_7nt_m4_vs_ref       	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_ref.tab
;	positions_7nt_m4_vs_ref_html  	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_ref.html
;	positions_7nt_m5_logo         	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_logo.png
;	positions_7nt_m5_logo_rc      	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_logo_rc.png
;	positions_7nt_m5_pssm_enrichment	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_scan_mkv1_enrichment.tab
;	positions_7nt_m5_pssm_enrichment_png	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_scan_mkv1_enrichment.png
;	positions_7nt_m5_pssm_site_distrib	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_site_distrib.tab
;	positions_7nt_m5_pssm_site_distrib_graph	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_site_distrib.png
;	positions_7nt_m5_pssm_sites   	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites.tab
;	positions_7nt_m5_pssm_sites_per_peak	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites_per_peak.tab
;	positions_7nt_m5_pssm_sites_per_peak_graph	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_sites_per_peak.png
;	positions_7nt_m5_tab          	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tab
;	positions_7nt_m5_tf           	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf
;	positions_7nt_m5_vs_db_jaspar_core_vertebrates	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_jaspar_core_vertebrates.tab
;	positions_7nt_m5_vs_db_jaspar_core_vertebrates_html	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_jaspar_core_vertebrates.html
;	positions_7nt_m5_vs_ref       	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_ref.tab
;	positions_7nt_m5_vs_ref_html  	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_ref.html
;	positions_7nt_pssm_counts     	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.txt
;	positions_7nt_pssm_logo1      	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m1.png
;	positions_7nt_pssm_logo2      	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m2.png
;	positions_7nt_pssm_logo3      	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m3.png
;	positions_7nt_pssm_logo4      	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m4.png
;	positions_7nt_pssm_logo5      	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m5.png
;	positions_7nt_pssm_logo_rc1   	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m1_rc.png
;	positions_7nt_pssm_logo_rc2   	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m2_rc.png
;	positions_7nt_pssm_logo_rc3   	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m3_rc.png
;	positions_7nt_pssm_logo_rc4   	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m4_rc.png
;	positions_7nt_pssm_logo_rc5   	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m5_rc.png
;	positions_7nt_pssm_sig        	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices.tf
;	positions_7nt_pssm_tf         	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf
;	small_summary                 	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/peak-motifs_small_summary.html
;	small_summary_txt             	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/reports/peak-motifs_small_summary.txt
;	synthesis                     	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/peak-motifs_synthesis.html
;	test_converted                	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta
;	test_purged                   	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta
;	test_seqlen                   	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_seqlen.tab
;	test_seqlen_distrib           	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_seqlen_distrib.tab
;	test_seqlen_distrib_graph     	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_seqlen_distrib.png
;	timelog                       	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/reports/peak-motifs_timelog.txt
;	timelog_html                  	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/reports/peak-motifs_timelog.html
;	timetable                     	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/reports/peak-motifs_timetable.txt

; 2015-11-03.070734
(cd $RSAT/public_html/tmp/www-data/2015/11/03 ;  zip -ryq peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/peak-motifs_archive.zip peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx -x peak-motifs_archive.zip)

