rsync -ruptl /var/www/html/rsat/perl-scripts/lib/js /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh
rsync -ruptl /var/www/html/rsat/public_html/images/program_icons/matrix-clustering_icons /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_query_matrices.transfac -from transfac -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/oct4_peak_motifs_permuted_input_motifs_processed_1.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/oct4_peak_motifs_permuted_input_motifs_processed_1.tf -from tf -to transfac -prefix_id oct4_peak_motifs_permuted -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/oct4_peak_motifs_permuted_input_motifs_processed.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/oct4_peak_motifs_permuted_input_motifs_processed.tf > /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -split -from tf -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/motif
cat /var/www/html/rsat/R-scripts/matrix-clustering.R | /usr/bin/R --slave --no-save --no-restore --no-environ --args " infile = '/var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/pairwise_compa.tab'; hclust.method = 'average'; description.file = '/var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab'; distance.table = '/var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/distance_table.tab'; alignment.file = '/var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/alignment_table.tab'; verbosity = 0; metric = 'Ncor'; heatmap.color.palette = 'YlOrRd'; heatmap.color.classes = '9'; export.newick = 0; radial.only = 0; draw.heatmap = 1; draw.consensus = 0; pos.hclust.in.heatmap = 'column'; lthsp = 'cor_0.6_Ncor_0.4_'; out.prefix = '/var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering'; "
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_1_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_1_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_2_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_2_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_3_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_3_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_4_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_4_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_5_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_5_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_6_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_6_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_7_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_7_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_8_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_8_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_9_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_9_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_10_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_10_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_11_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_11_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_12_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_12_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_13_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_13_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_14_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_14_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_15_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_15_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_16_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_16_transfac_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/cluster_17_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/cluster_17_transfac_motifs.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m14_local_words_7nt_m2_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_10/cluster_10_matrices_temp.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m16_positions_7nt_m1_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_11/cluster_11_matrices_temp.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m18_positions_7nt_m3_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m8_positions_6nt_m2_perm1_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_cat.tf
/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_matrices.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_11/cluster_11_matrices_temp.tf -from tf -to tf -attr name cluster_11 -attr accession cluster_11 -set_attr merged_AC 'oct4_peak_motifs_permuted:::positions_7nt_m1_perm1' -set_attr merged_ID 'positions_7nt_m1_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_11/cluster_11_matrices.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_10/cluster_10_matrices_temp.tf -from tf -to tf -attr name cluster_10 -attr accession cluster_10 -set_attr merged_AC 'oct4_peak_motifs_permuted:::local_words_7nt_m2_perm1' -set_attr merged_ID 'local_words_7nt_m2_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_10/cluster_10_matrices.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/IC_test_2026-05-11.053655_z70Psx
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_11/cluster_11_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_10/cluster_10_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m1_oligos_6nt_mkv4_m1_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_12/cluster_12_matrices_temp.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m13_local_words_7nt_m1_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_13/cluster_13_matrices_temp.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_12/cluster_12_matrices_temp.tf -from tf -to tf -attr name cluster_12 -attr accession cluster_12 -set_attr merged_AC 'oct4_peak_motifs_permuted:::oligos_6nt_mkv4_m1_perm1' -set_attr merged_ID 'oligos_6nt_mkv4_m1_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_12/cluster_12_matrices.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_13/cluster_13_matrices_temp.tf -from tf -to tf -attr name cluster_13 -attr accession cluster_13 -set_attr merged_AC 'oct4_peak_motifs_permuted:::local_words_7nt_m1_perm1' -set_attr merged_ID 'local_words_7nt_m1_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_13/cluster_13_matrices.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_13/cluster_13_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_12/cluster_12_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m17_positions_7nt_m2_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_14/cluster_14_matrices_temp.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m6_local_words_6nt_m3_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_15/cluster_15_matrices_temp.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_14/cluster_14_matrices_temp.tf -from tf -to tf -attr name cluster_14 -attr accession cluster_14 -set_attr merged_AC 'oct4_peak_motifs_permuted:::positions_7nt_m2_perm1' -set_attr merged_ID 'positions_7nt_m2_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_14/cluster_14_matrices.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_15/cluster_15_matrices_temp.tf -from tf -to tf -attr name cluster_15 -attr accession cluster_15 -set_attr merged_AC 'oct4_peak_motifs_permuted:::local_words_6nt_m3_perm1' -set_attr merged_ID 'local_words_6nt_m3_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_15/cluster_15_matrices.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_14/cluster_14_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_15/cluster_15_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m4_local_words_6nt_m1_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_16/cluster_16_matrices_temp.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m9_positions_6nt_m3_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_17/cluster_17_matrices_temp.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m19_dyads_m1_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m20_dyads_m2_perm1_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_cat.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_16/cluster_16_matrices_temp.tf -from tf -to tf -attr name cluster_16 -attr accession cluster_16 -set_attr merged_AC 'oct4_peak_motifs_permuted:::local_words_6nt_m1_perm1' -set_attr merged_ID 'local_words_6nt_m1_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_16/cluster_16_matrices.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_17/cluster_17_matrices_temp.tf -from tf -to tf -attr name cluster_17 -attr accession cluster_17 -set_attr merged_AC 'oct4_peak_motifs_permuted:::positions_6nt_m3_perm1' -set_attr merged_ID 'positions_6nt_m3_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_17/cluster_17_matrices.tf
/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_2 -name cluster_2 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_matrices.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_17/cluster_17_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_16/cluster_16_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/IC_test_2026-05-11.053658_dBxFCk
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m12_oligos_7nt_mkv5_m3_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices_temp.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m5_local_words_6nt_m2_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m7_positions_6nt_m1_perm1_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_cat.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices_temp.tf -from tf -to tf -attr name cluster_4 -attr accession cluster_4 -set_attr merged_AC 'oct4_peak_motifs_permuted:::oligos_7nt_mkv5_m3_perm1' -set_attr merged_ID 'oligos_7nt_mkv5_m3_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices.tf
/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_3 -name cluster_3 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_matrices.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/IC_test_2026-05-11.053659_jsEDUW
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m10_oligos_7nt_mkv5_m1_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_5/cluster_5_matrices_temp.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m11_oligos_7nt_mkv5_m2_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_6/cluster_6_matrices_temp.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_5/cluster_5_matrices_temp.tf -from tf -to tf -attr name cluster_5 -attr accession cluster_5 -set_attr merged_AC 'oct4_peak_motifs_permuted:::oligos_7nt_mkv5_m1_perm1' -set_attr merged_ID 'oligos_7nt_mkv5_m1_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_5/cluster_5_matrices.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_6/cluster_6_matrices_temp.tf -from tf -to tf -attr name cluster_6 -attr accession cluster_6 -set_attr merged_AC 'oct4_peak_motifs_permuted:::oligos_7nt_mkv5_m2_perm1' -set_attr merged_ID 'oligos_7nt_mkv5_m2_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_6/cluster_6_matrices.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_6/cluster_6_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_5/cluster_5_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m2_oligos_6nt_mkv4_m2_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_8/cluster_8_matrices_temp.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m15_local_words_7nt_m3_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m21_dyads_m3_perm1_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_7/merged_consensuses/node_1/cluster_7_node_1_cat.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_8/cluster_8_matrices_temp.tf -from tf -to tf -attr name cluster_8 -attr accession cluster_8 -set_attr merged_AC 'oct4_peak_motifs_permuted:::oligos_6nt_mkv4_m2_perm1' -set_attr merged_ID 'oligos_6nt_mkv4_m2_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_8/cluster_8_matrices.tf
/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_7/merged_consensuses/node_1/cluster_7_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_7 -name cluster_7 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_7/merged_consensuses/node_1/cluster_7_node_1_matrices.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_8/cluster_8_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_7/merged_consensuses/node_1/cluster_7_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/IC_test_2026-05-11.053701_Kzs3nE
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_7/merged_consensuses/node_1/cluster_7_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
cp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/oct4_peak_motifs_permuted_m3_oligos_6nt_mkv4_m3_perm1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_9/cluster_9_matrices_temp.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_9/cluster_9_matrices_temp.tf -from tf -to tf -attr name cluster_9 -attr accession cluster_9 -set_attr merged_AC 'oct4_peak_motifs_permuted:::oligos_6nt_mkv4_m3_perm1' -set_attr merged_ID 'oligos_6nt_mkv4_m3_perm1' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_9/cluster_9_matrices.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_clusters_information/cluster_9/cluster_9_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
rm -r /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_pairwise_compa_logos
cp /var/www/html/rsat/public_html/templates_html/display_d3_tree.html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_logo_tree.html
cp /var/www/html/rsat/public_html/templates_html/display_small_d3_tree.html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_portable_logo_tree.html
mv /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_temporary.html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_logo_tree.html
mv /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_portable_logo_tree.html
/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_html/pairwise_compa_matrix_descriptions.html
/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/distance_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/distance_table.html
/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/alignment_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/alignment_table.html
/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/clusters.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/clusters.html
/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/clusters_motif_names.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/clusters_motif_names.html
mv -f /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_portable_logo_tree.html
; matrix-clustering -v 1 -max_matrices 300 -matrix oct4_peak_motifs_permuted $RSAT/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_query_matrices.transfac transfac -hclust_method average -calc sum -title clustering_column-permuted_matrices_discovered_in_oct4_chip-seq -metric_build_tree Ncor -lth w 5 -lth cor 0.6 -lth Ncor 0.4 -quick -label_in_tree name -return json,heatmap -o $RSAT/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering
; Program version 1.05
; Number of matrices 21
; Output files
; motif_richness_tsv /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_motif_richness.tsv
; pairwise_compa /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/pairwise_compa.tab
; hexa_colors /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_hexa_colors.txt
; log /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_log.txt
; clusters_table_motif_names /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/clusters_motif_names.tab
; heatmap_collections_attributes /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/collection_heatmap_order.tab
; internal_nodes_attributes_table /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/internal_nodes_attributes.tab
; heatmap_coverage_d3 /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/convergency_heatmap_tab.tsv
; motif_richness_barplot_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_motif_richness_barplot.html
; clusters_table /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/clusters.tab
; alignment_table /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/alignment_table.tab
; consensus_cladogram_json /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_trees/tree.json
; small_forest_export /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_small_forest.html
; reference_compa_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_html/Root_vs_reference_collection_compa.html
; reference_compa /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/Root_vs_reference_collection_compa.tab
; central_motifs_IDs_temp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_central_motifs_IDs_temporal.tab
; alignment_table_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/alignment_table.html
; clusters_table_motif_names_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/clusters_motif_names.html
; dynamic_heatmap_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_dynamic_heatmap.html
; coverage_table /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/clusters_summary_coverage_contingency_table.tab
; distance_table /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/distance_table.tab
; nb_clusters_table /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/number_of_clusters.tab
; temp_html_3 /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_temporary_3.html
; summary_temp /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_SUMMARY_TEMP.html
; archive /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_archive.zip
; matrix_descriptions_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_html/pairwise_compa_matrix_descriptions.html
; all_concatenated_motifs /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
; central_motifs_tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_central_motifs_transfac.tf
; int_align /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/intermediate_alignments.tab
; html_index /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_html/index.html
; heatmap_coverage_attributes /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/convergency_heatmap_attributes.tab
; root_motifs /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_cluster_root_motifs.tf
; matrix_descriptions /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab
; coverage_json_folder /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_coverage_json
; small_logo_cladogram_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_portable_logo_tree.html
; Rlog /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_Rlog.txt
; temp_html_2 /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_temporary_2.html
; logo_cladogram_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_logo_tree.html
; clusters_table_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/clusters.html
; central_motifs /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_central_motifs_IDs.tab
; prefix /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering
; temp_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_temporary.html
; motif_file /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf
; cluster_summary_table /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/clusters_summary_table.tab
; radial_tree_template /var/www/html/rsat/public_html/templates_html/Radial_tree_template.html
; pairwise_compa_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_html/pairwise_compa.html
; summary /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_SUMMARY.html
; heatmap_jpg /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_figures/heatmap.jpg
; percent_table /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/clusters_summary_percent_table.tab
; cluster_IDs_names /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_cluster_IDs.txt
; heatmap_collections_d3 /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/collection_heatmap_tab.tsv
; ref_collection_tf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_reference_collection.tf
; dynamic_coverage_heatmap_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_dynamic_coverage_heatmap.html
; err_log /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_errors.txt
; radial_tree /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_radial_tree.html
; heatmap_pdf /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_figures/heatmap.pdf
; distance_table_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_tables/distance_table.html
; root_motifs_table /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_root_motifs_table.tab
; input_matrices /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data/input_motifs_processed.tf
; Directories
; data /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_data
; output /var/www/html/rsat/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh
; Host name rsat
; Job started 2026-05-11.053642
; Job done 2026-05-11.053704
; Seconds 0.76
; user 0.76
; system 0.33
; cuser 24.91
; csystem 5.7