; matrix-from-patterns  -v 1 -seq $RSAT/public_html/tmp/www-data/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged -subst 1 -maxfl 1 -max_asmb_size 30 -pl $RSAT/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_clusters_complete_k5.tab -sc 4 -cc 2 -max_asmb_per_cluster 5 -flanks 2 -logo -cluster sig -o $RSAT/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm
; Input files
;	patterns	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_clusters_complete_k5.tab
;	sequence	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged
; Output files
;	sig_matrices_split	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split_matrix_list.tab
;	output	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm
;	sig_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices.tf
;	gibbs_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_gibbs_matrices.txt
;	err	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_err.txt
;	count_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_count_matrices.txt
;	count_matrices_tf	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_count_matrices.tf
;	sig_sites	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_sites.ft
;	assembly	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm.asmb
;	log	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_log.txt
;	logo_basename	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_count_matrices_logo
;	links	/var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_count_matrices_links.txt
; Number of patterns	138
; patterns -> assemblies
/var/www/html/rsat/perl-scripts/pattern-assembly -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_clusters_complete_k5.tab -2str -maxfl 1 -subst 1 -max_asmb_width 25 -toppat 100 -max_asmb_size 30 -max_asmb_width 25 -sc 4 -cc 2 -max_asmb_per_cluster 5 -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm.asmb


/var/www/html/rsat/perl-scripts/pattern-assembly -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_clusters_complete_k5.tab -2str -maxfl 1 -subst 1 -max_asmb_width 25 -toppat 100 -max_asmb_size 30 -max_asmb_width 25 -sc 4 -cc 2 -max_asmb_per_cluster 5 -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm.asmb
; Number of assemblies	15
; Number of assembled patterns	91
; assemblies -> significance matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 10 -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 10 -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_nr


/var/www/html/rsat/perl-scripts/convert-matrix -from tf -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_nr_cluster_root_motifs.tf -to tab -split  -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split; rm -f /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged -m /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split_cluster_3.tab -name cluster_3 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged -m /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split_cluster_3.tab -name cluster_3 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged -m /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split_cluster_2.tab -name cluster_2 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged -m /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split_cluster_2.tab -name cluster_2 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged -m /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split_cluster_1.tab -name cluster_1 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged -m /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split_cluster_1.tab -name cluster_1 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged -m /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split_cluster_4.tab -name cluster_4 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged -m /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split_cluster_4.tab -name cluster_4 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged -m /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split_cluster_5.tab -name cluster_5 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/retrieve-seq_2025-08-14.161845_1GRfpB.fasta.fasta.purged -m /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_matrices_split_cluster_5.tab -name cluster_5 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_sites.ft -from feature -to transfac -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_count_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 0 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_sites.ft -from feature -to transfac -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_count_matrices.tf -from transfac -to tab -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_count_matrices.txt


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_count_matrices.tf -from transfac -to tab -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_count_matrices_logo -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_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/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_count_matrices_logo -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_count_matrices_links.txt


rm -f /var/www/html/rsat/public_html/tmp/www-data/2025/08/14/position-analysis_2025-08-14.163228_RqWWHk/position-analysis_pssm_sig_sites.ft
; Host name	rsat
; Job started	2025-08-14.163320
; Job done	2025-08-14.163339
; Seconds	0.1
;	user	0.1
;	system	0.01
;	cuser	15.56
;	csystem	2.01