; matrix-from-patterns  -v 1 -seq /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -pl /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab -bgfile /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 50 -max_asmb_nb 3 -subst 1 -prefix oligos_6nt_mkv4 -flanks 2 -collect_method matrix-scan-quick -logo -o /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm
; Input files
;	patterns	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab
;	sequence	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta
; Output files
;	sig_matrices_split	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_sig_matrices_split
;	sig_matrices	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_sig_matrices.tf
;	count_matrices	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices.txt
;	logo_basename	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices_logo
;	count_matrices_tf	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices.tf
;	gibbs_matrices	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_gibbs_matrices.txt
;	sig_sites	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_sig_sites.ft
;	output	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm
;	log	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_log.txt
;	assembly	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm.asmb
;	links	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices_links.txt
; Number of patterns	50
; patterns -> assemblies
/home/rsat/rsa-tools/perl-scripts/pattern-assembly -v 1 -i /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab -2str -maxfl 1 -subst 1 -toppat 50 -max_asmb_size 50 -max_asmb_nb 3 -o /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm.asmb
; Number of assemblies	3
; Number of assembled patterns	5
; assemblies -> significance matrices
/home/rsat/rsa-tools/perl-scripts/convert-matrix -v 1 -i /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm.asmb -from assembly -to tf -return counts -flanks 2 -top 3 -o /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_sig_matrices.tf
; significance matrices + sequences -> sites
/home/rsat/rsa-tools/bin/matrix-scan-quick -v 1 -i /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -m /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_sig_matrices_split_m1.tab -name oligos_6nt_mkv4_m0 -2str -t 7 -return sites -bgfile /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_sig_sites.ft
; significance matrices + sequences -> sites
/home/rsat/rsa-tools/bin/matrix-scan-quick -v 1 -i /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -m /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_sig_matrices_split_m2.tab -name oligos_6nt_mkv4_m1 -2str -t 7 -return sites -bgfile /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_sig_sites.ft
; significance matrices + sequences -> sites
/home/rsat/rsa-tools/bin/matrix-scan-quick -v 1 -i /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -m /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_sig_matrices_split_m3.tab -name oligos_6nt_mkv4_m2 -2str -t 7 -return sites -bgfile /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_sig_sites.ft
; sites -> transfac matrices
/home/rsat/rsa-tools/perl-scripts/convert-matrix -v 0 -i /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_sig_sites.ft -from feature -to transfac -prefix oligos_6nt_mkv4 -return counts -return logo -logo_format png,pdf  -logo_file /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices_logo -o /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices.tf
; transfac-formatted -> tab-formatted matrices
/home/rsat/rsa-tools/perl-scripts/convert-matrix -v 1 -i /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices.tf -from transfac -to tab -return counts -o /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices.txt
; sites -> count matrices
/home/rsat/rsa-tools/perl-scripts/convert-matrix -v 1 -i /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices.txt -from tab -to tab -return counts -return logo -logo_format png,pdf -logo_file /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices_logo -o /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices_links.txt
; Host name	rsat
; Job started	2012_03_11.082938
; Job done	2012_03_11.083002
; Seconds	0.11
;	user	0.11
;	system	0.01
;	cuser	22.94
;	csystem	0.56
