; matrix-from-patterns  -v 1 -seq $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.tab -bgfile $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_6nt_mkv3 -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm
; Input files
;	sequence	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta
;	patterns	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.tab
; Output files
;	count_matrices	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices.txt
;	count_matrices_tf	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices.tf
;	sig_sites	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_sites.ft
;	gibbs_matrices	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_gibbs_matrices.txt
;	assembly	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm.asmb
;	output	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm
;	links	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices_links.txt
;	logo_basename	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices_logo
;	sig_matrices_split	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_matrices_split_matrix_list.tab
;	log	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_log.txt
;	sig_matrices	/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_matrices.tf
; Number of patterns	42
; patterns -> assemblies
/workspace/rsat/perl-scripts/pattern-assembly -v 1 -i /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.tab -2str -maxfl 1 -subst 1 -max_asmb_width 20 -toppat 100 -max_asmb_size 50 -max_asmb_width 20 -max_asmb_nb 5 -o /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm.asmb
; Number of assemblies	5
; Number of assembled patterns	14
; assemblies -> significance matrices
/workspace/rsat/perl-scripts/convert-matrix -v 1 -i /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm.asmb -from assembly -to tf -return counts -flanks 2 -top 5 -prefix oligos_6nt_mkv3 -o /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_matrices.tf

; significance matrices + sequences -> sites
/workspace/rsat/bin/matrix-scan-quick -v 1 -i /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -m /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_matrices_split_oligos_6nt_mkv3_m1.tab -name oligos_6nt_mkv3_m1 -2str -t 7 -return sites -bgfile /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/workspace/rsat/bin/matrix-scan-quick -v 1 -i /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -m /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_matrices_split_oligos_6nt_mkv3_m2.tab -name oligos_6nt_mkv3_m2 -2str -t 7 -return sites -bgfile /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/workspace/rsat/bin/matrix-scan-quick -v 1 -i /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -m /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_matrices_split_oligos_6nt_mkv3_m3.tab -name oligos_6nt_mkv3_m3 -2str -t 7 -return sites -bgfile /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/workspace/rsat/bin/matrix-scan-quick -v 1 -i /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -m /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_matrices_split_oligos_6nt_mkv3_m4.tab -name oligos_6nt_mkv3_m4 -2str -t 7 -return sites -bgfile /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/workspace/rsat/bin/matrix-scan-quick -v 1 -i /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000.fasta -m /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_matrices_split_oligos_6nt_mkv3_m5.tab -name oligos_6nt_mkv3_m5 -2str -t 7 -return sites -bgfile /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_sites.ft
; sites -> transfac matrices
/workspace/rsat/perl-scripts/convert-matrix -v 0 -i /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_sig_sites.ft -from feature -to transfac -prefix oligos_6nt_mkv3 -return counts -return logo -logo_format png  -logo_file /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices_logo -o /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices.tf
; transfac-formatted -> tab-formatted matrices
/workspace/rsat/perl-scripts/convert-matrix -v 1 -i /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices.tf -from transfac -to tab -return counts -o /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices.txt
; sites -> count matrices
/workspace/rsat/perl-scripts/convert-matrix -v 1 -i /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices.tf -from tf -to tab -return counts -return logo -logo_format png -logo_file /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices_logo -o /workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3_pssm_count_matrices_links.txt
; Host name	rsat-tagc
; Job started	2015-11-03.065605
; Job done	2015-11-03.065618
; Seconds	0.26
;	user	0.26
;	system	0.05
;	cuser	12.4
;	csystem	0.94
