; matrix-from-patterns  -v 1 -logo -seq $RSAT/public_html/tmp/www-data/2025/01/22/tmp_sequence_2025-01-22.073040_2NsSul.fasta -format fasta -asmb $RSAT/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w.asmb -min_weight 5 -flanks 2 -max_asmb_nb 20 -cluster sig -uth Pval 0.00025 -bginput -markov 0 -o $RSAT/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm
; Input files
;	sequence	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/tmp_sequence_2025-01-22.073040_2NsSul.fasta
;	assembly	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w.asmb
; Output files
;	err	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_err.txt
;	count_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices.txt
;	sig_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices.tf
;	logo_basename	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices_logo
;	log	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_log.txt
;	sig_matrices_split	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices_split_matrix_list.tab
;	gibbs_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_gibbs_matrices.txt
;	output	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm
;	links	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices_links.txt
;	sig_sites	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_sites.ft
;	assembly	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w.asmb
;	count_matrices_tf	/var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices.tf
; Number of assemblies	12
; Number of assembled patterns	38
; assemblies -> significance matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 20 -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 20 -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_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/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 10 -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_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/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 10 -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices_rescaled.tf
; significance matrices -> non-redundant matrices
/var/www/html/rsat/perl-scripts/matrix-clustering -v 0 -matrix sig /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices_rescaled.tf tf -lth Ncor 0.4 -lth cor 0.6 -lth w 5 -calc sum -hclust_method average -label_in_tree name -metric_build_tree Ncor -return root_matrices -quick -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices_nr


/var/www/html/rsat/perl-scripts/matrix-clustering -v 0 -matrix sig /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices_rescaled.tf tf -lth Ncor 0.4 -lth cor 0.6 -lth w 5 -calc sum -hclust_method average -label_in_tree name -metric_build_tree Ncor -return root_matrices -quick -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices_nr


/var/www/html/rsat/perl-scripts/convert-matrix -from tf -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices_nr_cluster_root_motifs.tf -to tab -split  -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_matrices_split; rm -f /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices.txt
; sites -> transfac matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 0 -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_sites.ft -from feature -to transfac -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 0 -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_sig_sites.ft -from feature -to transfac -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_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/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices.tf -from transfac -to tab -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices.txt


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices.tf -from transfac -to tab -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_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/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices.tf -from tf -to tab -return counts -return logo -logo_format png -logo_file /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices_logo -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_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/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices.tf -from tf -to tab -return counts -return logo -logo_format png -logo_file /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices_logo -o /var/www/html/rsat/public_html/tmp/www-data/2025/01/22/dyad-analysis_2025-01-22.073040_37721w_pssm_count_matrices_links.txt
; Host name	rsat
; Job started	2025-01-22.073044
; Job done	2025-01-22.073046
; Seconds	0.1
;	user	0.1
;	system	0.01
;	cuser	1.68
;	csystem	0.35