; matrix-from-patterns  -v 1 -seq $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -asmb $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.asmb -prefix lexA -format fasta -sites -uth Pval 0.00025 -bginput -markov 0 -flanks 2 -2str -logo -o $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm
; Input files
;	sequence	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta
;	assembly	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.asmb
; Output files
;	sig_matrices_split	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split_matrix_list.tab
;	sig_matrices	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices.tf
;	count_matrices	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.txt
;	logo_basename	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices_logo
;	count_matrices_tf	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.tf
;	gibbs_matrices	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_gibbs_matrices.txt
;	sig_sites	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft
;	err	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_err.txt
;	output	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm
;	log	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_log.txt
;	links	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices_links.txt
;	assembly	/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.asmb
; Number of assemblies	5
; Number of assembled patterns	102
; assemblies -> significance matrices
/space23/rsat/perl-scripts/convert-matrix -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.asmb -from assembly -to tf -return counts -flanks 2 -top 5 -prefix lexA -o /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices.tf


/space23/rsat/perl-scripts/convert-matrix -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.asmb -from assembly -to tf -return counts -flanks 2 -top 5 -prefix lexA -o /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices.tf
; Rescaling significance matrices
/space23/rsat/perl-scripts/convert-matrix -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices.tf -from tf -to tf -return counts -rescale 10 -o /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_rescaled.tf


/space23/rsat/perl-scripts/convert-matrix -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices.tf -from tf -to tf -return counts -rescale 10 -o /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_rescaled.tf


/space23/rsat/perl-scripts/convert-matrix  -from tf -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_rescaled.tf -to tab -split  -o /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split; rm -f /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.txt

; significance matrices + sequences -> sites
/space23/rsat/bin/matrix-scan-quick -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -m /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split_lexA_m1.tab -name lexA_m1 -2str -t 5 -return sites >> /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft


/space23/rsat/bin/matrix-scan-quick -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -m /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split_lexA_m1.tab -name lexA_m1 -2str -t 5 -return sites >> /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/space23/rsat/bin/matrix-scan-quick -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -m /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split_lexA_m2.tab -name lexA_m2 -2str -t 5 -return sites >> /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft


/space23/rsat/bin/matrix-scan-quick -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -m /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split_lexA_m2.tab -name lexA_m2 -2str -t 5 -return sites >> /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/space23/rsat/bin/matrix-scan-quick -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -m /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split_lexA_m3.tab -name lexA_m3 -2str -t 5 -return sites >> /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft


/space23/rsat/bin/matrix-scan-quick -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -m /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split_lexA_m3.tab -name lexA_m3 -2str -t 5 -return sites >> /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/space23/rsat/bin/matrix-scan-quick -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -m /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split_lexA_m4.tab -name lexA_m4 -2str -t 5 -return sites >> /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft


/space23/rsat/bin/matrix-scan-quick -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -m /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split_lexA_m4.tab -name lexA_m4 -2str -t 5 -return sites >> /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/space23/rsat/bin/matrix-scan-quick -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -m /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split_lexA_m5.tab -name lexA_m5 -2str -t 5 -return sites >> /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft


/space23/rsat/bin/matrix-scan-quick -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -m /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_matrices_split_lexA_m5.tab -name lexA_m5 -2str -t 5 -return sites >> /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft
; sites -> transfac matrices
/space23/rsat/perl-scripts/convert-matrix -v 0 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft -from feature -to transfac -prefix lexA -return counts -return sites -return logo -logo_format png  -logo_file /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices_logo -o /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.tf


/space23/rsat/perl-scripts/convert-matrix -v 0 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft -from feature -to transfac -prefix lexA -return counts -return sites -return logo -logo_format png  -logo_file /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices_logo -o /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.tf
; transfac-formatted -> tab-formatted matrices
/space23/rsat/perl-scripts/convert-matrix -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.tf -from transfac -to tab -return counts -return sites -o /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.txt


/space23/rsat/perl-scripts/convert-matrix -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.tf -from transfac -to tab -return counts -return sites -o /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.txt
; sites -> count matrices
/space23/rsat/perl-scripts/convert-matrix -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.tf -from tf -to tab -return counts -return sites -return logo -logo_format png -logo_file /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices_logo -o /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices_links.txt


/space23/rsat/perl-scripts/convert-matrix -v 1 -i /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.tf -from tf -to tab -return counts -return sites -return logo -logo_format png -logo_file /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices_logo -o /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices_links.txt


rm -f /space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_sig_sites.ft
; Host name	sinik
; Job started	2018-03-21.142947
; Job done	2018-03-21.143009
; Seconds	0.28
;	user	0.28
;	system	0.02
;	cuser	19.42
;	csystem	1.25
