; matrix-from-patterns  -v 1 -sites -seq $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test.fasta -pl $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -bgfile $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 0 -prefix dyads -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm
; Input files
;	sequence	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test.fasta
;	patterns	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab
; Output files
;	assembly	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
;	gibbs_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_gibbs_matrices.txt
;	output	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm
;	count_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.txt
;	count_matrices_tf	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf
;	sig_matrices_split	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_matrix_list.tab
;	log	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt
;	sig_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices.tf
;	sig_sites	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft
;	logo_basename	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo
;	err	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_err.txt
;	links	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_links.txt
; Number of patterns	3
; patterns -> assemblies
/var/www/html/rsat/perl-scripts/pattern-assembly -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -2str -maxfl 1 -subst 0 -max_asmb_width 20 -toppat 100 -max_asmb_size 50 -max_asmb_width 20 -max_asmb_nb 5 -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb


/var/www/html/rsat/perl-scripts/pattern-assembly -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -2str -maxfl 1 -subst 0 -max_asmb_width 20 -toppat 100 -max_asmb_size 50 -max_asmb_width 20 -max_asmb_nb 5 -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
; Number of assemblies	3
; Number of assembled patterns	3
; assemblies -> significance matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 5 -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 5 -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices.tf
; Rescaling significance matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 10 -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_rescaled.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 10 -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_rescaled.tf


/var/www/html/rsat/perl-scripts/convert-matrix -from tf -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_rescaled.tf -to tab -split  -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split; rm -f /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.txt

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_assembly_1.tab -name dyads_m1 -2str -t 5 -return sites -bgfile /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_assembly_1.tab -name dyads_m1 -2str -t 5 -return sites -bgfile /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_assembly_2.tab -name dyads_m2 -2str -t 5 -return sites -bgfile /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_assembly_2.tab -name dyads_m2 -2str -t 5 -return sites -bgfile /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_assembly_3.tab -name dyads_m3 -2str -t 5 -return sites -bgfile /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_assembly_3.tab -name dyads_m3 -2str -t 5 -return sites -bgfile /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft
; sites -> transfac matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 0 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft -from feature -to transfac -return counts -return sites -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 0 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft -from feature -to transfac -return counts -return sites -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf
; transfac-formatted -> tab-formatted matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf -from transfac -to tab -return counts -return sites -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.txt


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf -from transfac -to tab -return counts -return sites -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.txt
; sites -> count matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf -from tf -to tab -return counts -return sites -return logo -logo_format png -logo_file /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_links.txt


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf -from tf -to tab -return counts -return sites -return logo -logo_format png -logo_file /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_links.txt
; Host name	rsat
; Job started	2025-03-02.091159
; Job done	2025-03-02.091201
; Seconds	0.09
;	user	0.09
;	system	0.02
;	cuser	1.71
;	csystem	0.26
