; Sequence sets (name, permutations, file)
; 2019-06-03.161044	Computing score distribution
;	Sequence type         	matrix_sites
;	Sequence file         	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_sites.fasta
;	Type-specific options 	 -uth rank_pm 1 -1str
; Command:
/space23/rsat/perl-scripts/matrix-scan -v 1 -matrix_format tab -bg_format inclusive -i /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_sites.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str  -uth rank_pm 1 -1str -return sites | grep -v '^;' | grep -v '^#' | cut -f 8  | /space23/rsat/perl-scripts/classfreq -v 1 -ci 0.1 -min -50.0 | cut -f 1,4,5,6,9  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_matrix_sites_score_distrib.tab


; 2019-06-03.161044	Computing score distribution
;	Sequence type         	allup-noorf
;	Sequence file         	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
; Command:
/state/partition1/space23/rsat/bin/matrix-scan-quick -i /home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str -return distrib  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_score_distrib.tab


; 2019-06-03.161046	Computing score distribution
;	Sequence type         	allup-noorf_perm_col_1
;	Sequence file         	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
; Command:
/state/partition1/space23/rsat/bin/matrix-scan-quick -i /home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_1.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str -return distrib  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_1_score_distrib.tab


; 2019-06-03.161048	Computing score distribution
;	Sequence type         	allup-noorf_perm_col_2
;	Sequence file         	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
; Command:
/state/partition1/space23/rsat/bin/matrix-scan-quick -i /home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_2.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str -return distrib  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_2_score_distrib.tab


; 2019-06-03.161049	Computing score distribution
;	Sequence type         	allup-noorf_perm_col_3
;	Sequence file         	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
; Command:
/state/partition1/space23/rsat/bin/matrix-scan-quick -i /home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_3.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str -return distrib  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_3_score_distrib.tab


; 2019-06-03.161051	Computing score distribution
;	Sequence type         	allup-noorf_perm_col_4
;	Sequence file         	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
; Command:
/state/partition1/space23/rsat/bin/matrix-scan-quick -i /home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_4.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str -return distrib  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_4_score_distrib.tab


; 2019-06-03.161052	Computing score distribution
;	Sequence type         	allup-noorf_perm_col_5
;	Sequence file         	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
; Command:
/state/partition1/space23/rsat/bin/matrix-scan-quick -i /home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_5.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str -return distrib  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_5_score_distrib.tab


; 2019-06-03.161053	Computing score distribution
;	Sequence type         	allup-noorf_perm_col_6
;	Sequence file         	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
; Command:
/state/partition1/space23/rsat/bin/matrix-scan-quick -i /home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_6.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str -return distrib  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_6_score_distrib.tab


; 2019-06-03.161054	Computing score distribution
;	Sequence type         	allup-noorf_perm_col_7
;	Sequence file         	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
; Command:
/state/partition1/space23/rsat/bin/matrix-scan-quick -i /home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_7.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str -return distrib  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_7_score_distrib.tab


; 2019-06-03.161056	Computing score distribution
;	Sequence type         	allup-noorf_perm_col_8
;	Sequence file         	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
; Command:
/state/partition1/space23/rsat/bin/matrix-scan-quick -i /home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_8.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str -return distrib  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_8_score_distrib.tab


; 2019-06-03.161057	Computing score distribution
;	Sequence type         	allup-noorf_perm_col_9
;	Sequence file         	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
; Command:
/state/partition1/space23/rsat/bin/matrix-scan-quick -i /home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_9.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str -return distrib  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_9_score_distrib.tab


; 2019-06-03.161059	Computing score distribution
;	Sequence type         	allup-noorf_perm_col_10
;	Sequence file         	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
; Command:
/state/partition1/space23/rsat/bin/matrix-scan-quick -i /home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -m /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_10.tab -pseudo 1 -decimals 1 -bgfile /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -2str -return distrib  > /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_10_score_distrib.tab

;
; XYgraph command
/space23/rsat/perl-scripts/XYgraph   -i /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa.tab -format png -lines -pointsize 0   -title1 ModE -xgstep1 5 -xgstep2 1 -ymin 1.0e-7 -ymax 1 -xmin -50 -xmax 30 -xcol 1 -ycol 2,3,4,5 -ymin 0  -ymax 1  -xgstep1 5 -xgstep2 1 -ygstep1 0.1 -ygstep2 0.02 -gp 'set size ratio 0.5'   -null '<NULL>'  -title1 'CGHTATAYACWWVMYTAYAYASCGHWA' -legend  -xsize 800 -ysize 400  -xleg1 'matrix score'  -yleg1 'dCDF (log scale)'    -o /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa.png
;
; XYgraph command
/space23/rsat/perl-scripts/XYgraph   -i /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa.tab -format png -lines -pointsize 0   -title1 ModE -xgstep1 5 -xgstep2 1 -ymin 1.0e-7 -ymax 1 -xmin -50 -xmax 30 -xcol 1 -ycol 2,3,4,5 -xgstep1 5 -xgstep2 1 -ymax 1 -ylog 10 -gp 'set size ratio 0.5'  -null '<NULL>'  -title1 'CGHTATAYACWWVMYTAYAYASCGHWA' -legend  -xsize 800 -ysize 400  -xleg1 'matrix score'  -yleg1 'dCDF (log scale)'    -o /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa_logy.png
;
; XYgraph command
/space23/rsat/perl-scripts/XYgraph -xlog 10   -i /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa.tab -format png -lines -pointsize 0   -title1 ModE -xgstep1 5 -xgstep2 1 -ymin 1.0e-7 -ymax 1 -xmin -50 -xmax 30 -xcol 2 -ycol 2,3,4,5 -ygstep1 0.1 -ygstep2 0.02 -null '<NULL>'  -ymax 1  -xmax 1  -title1 'CGHTATAYACWWVMYTAYAYASCGHWA' -legend  -xsize 800 -ysize 400  -xleg1 'matrix score'  -yleg1 'dCDF (log scale)'   -gstep1 0.1 -gstep2 0.05 -title1 ModE -o /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa_roc_xlog.png -xleg1 'FPR (Reference = theor)'  -yleg1 'Site Sn + other distributions' 
;
; XYgraph command
/space23/rsat/perl-scripts/XYgraph   -i /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa.tab -format pdf -lines -pointsize 0   -title1 ModE -xgstep1 5 -xgstep2 1 -ymin 1.0e-7 -ymax 1 -xmin -50 -xmax 30 -xcol 1 -ycol 2,3,4,5 -ymin 0  -ymax 1  -xgstep1 5 -xgstep2 1 -ygstep1 0.1 -ygstep2 0.02 -gp 'set size ratio 0.5'   -null '<NULL>'  -title1 'CGHTATAYACWWVMYTAYAYASCGHWA' -legend  -xsize 800 -ysize 400  -xleg1 'matrix score'  -yleg1 'dCDF (log scale)'    -o /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa.pdf
;
; XYgraph command
/space23/rsat/perl-scripts/XYgraph   -i /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa.tab -format pdf -lines -pointsize 0   -title1 ModE -xgstep1 5 -xgstep2 1 -ymin 1.0e-7 -ymax 1 -xmin -50 -xmax 30 -xcol 1 -ycol 2,3,4,5 -xgstep1 5 -xgstep2 1 -ymax 1 -ylog 10 -gp 'set size ratio 0.5'  -null '<NULL>'  -title1 'CGHTATAYACWWVMYTAYAYASCGHWA' -legend  -xsize 800 -ysize 400  -xleg1 'matrix score'  -yleg1 'dCDF (log scale)'    -o /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa_logy.pdf
;
; XYgraph command
/space23/rsat/perl-scripts/XYgraph -xlog 10   -i /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa.tab -format pdf -lines -pointsize 0   -title1 ModE -xgstep1 5 -xgstep2 1 -ymin 1.0e-7 -ymax 1 -xmin -50 -xmax 30 -xcol 2 -ycol 2,3,4,5 -ygstep1 0.1 -ygstep2 0.02 -null '<NULL>'  -ymax 1  -xmax 1  -title1 'CGHTATAYACWWVMYTAYAYASCGHWA' -legend  -xsize 800 -ysize 400  -xleg1 'matrix score'  -yleg1 'dCDF (log scale)'   -gstep1 0.1 -gstep2 0.05 -title1 ModE -o /home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa_roc_xlog.pdf -xleg1 'FPR (Reference = theor)'  -yleg1 'Site Sn + other distributions' 
; Input files
;	bg_file                      	/space23/rsat/public_html/data/genomes/Escherichia_coli_GCF_000005845.2_ASM584v2/oligo-frequencies/2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz
;	matrix                       	/home/cjgonzal/data/Matrices_NR/ModE/ModE.EcolK12_2nt_upstream.27.meme
;	matrix_sites                 	/home/cjgonzal/data/Matrices_NR/ModE/ModE.EcolK12_2nt_upstream.27.meme
; Sequence files
;	allup-noorf                  	/home/cjgonzal/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta
;	matrix_sites                 	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_sites.fasta
; Output files
;	allup-noorf_10perm           	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_10perm_score_distrib.tab
;	bg_file_inclusive            	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
;	distrib_compa                	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_score_distrib_compa
;	empirical_distrib_allup-noorf	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_score_distrib.tab
;	empirical_distrib_allup-noorf_perm_col_1	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_1_score_distrib.tab
;	empirical_distrib_allup-noorf_perm_col_10	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_10_score_distrib.tab
;	empirical_distrib_allup-noorf_perm_col_2	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_2_score_distrib.tab
;	empirical_distrib_allup-noorf_perm_col_3	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_3_score_distrib.tab
;	empirical_distrib_allup-noorf_perm_col_4	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_4_score_distrib.tab
;	empirical_distrib_allup-noorf_perm_col_5	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_5_score_distrib.tab
;	empirical_distrib_allup-noorf_perm_col_6	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_6_score_distrib.tab
;	empirical_distrib_allup-noorf_perm_col_7	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_7_score_distrib.tab
;	empirical_distrib_allup-noorf_perm_col_8	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_8_score_distrib.tab
;	empirical_distrib_allup-noorf_perm_col_9	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_perm_col_9_score_distrib.tab
;	empirical_distrib_matrix_sites	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_matrix_sites_score_distrib.tab
;	log                          	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality_log.txt
;	matrix_info                  	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_info.txt
;	matrix_log                   	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_log.txt
;	matrix_logo                  	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_logo
;	matrix_logo_png              	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_logo_m1.png
;	matrix_logo_rc_png           	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_logo_m1_rc.png
;	matrix_perm_col_1            	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_1.tab
;	matrix_perm_col_10           	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_10.tab
;	matrix_perm_col_2            	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_2.tab
;	matrix_perm_col_3            	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_3.tab
;	matrix_perm_col_4            	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_4.tab
;	matrix_perm_col_5            	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_5.tab
;	matrix_perm_col_6            	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_6.tab
;	matrix_perm_col_7            	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_7.tab
;	matrix_perm_col_8            	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_8.tab
;	matrix_perm_col_9            	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_perm_col_9.tab
;	matrix_sites                 	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_sites.fasta
;	matrix_synthesis             	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_synthesis.html
;	matrix_tab                   	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix.tab
;	matrix_theoretical_distrib   	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_theor_score_distrib.tab
;	matrix_transfac              	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix.tf
;	perm_col_matrices_allup-noorf_10perm	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_allup-noorf_matrix_perm_col_all_10.tab
;	perm_col_matrices_matrix_sites_0perm	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_matrix_sites_matrix_perm_col_all_0.tab
;	synthesis                    	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/ModE.EcolK12_2nt_upstream.27.meme_quality_synthesis.html
; Directories
;	matrix_output                	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA
;	output                       	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme
; Matrix permutations per sequence type
;	matrix_sites         	0
;	allup-noorf          	10
; Distributions
;	1                    	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_matrix_sites_score_distrib.tab
;	2                    	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_score_distrib.tab
;	3                    	/home/cjgonzal/results/manual/matrix_quality_20190329/ModE/ModE.EcolK12_2nt_upstream.27.meme/CGHTATAYACWWVMYTAYAYASCGHWA/ModE.EcolK12_2nt_upstream.27.meme_quality_scan_allup-noorf_10perm_score_distrib.tab
; Host name	sinik
; Job started	2019-06-03.161028
; Job done	2019-06-03.161110
; Seconds	0.63
;	user	0.63
;	system	0.13
;	cuser	40.46
;	csystem	1.99