

rsync -ruptl /var/www/html/rsat/perl-scripts/lib/js /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ


rsync -ruptl /var/www/html/rsat/public_html/images/program_icons/matrix-clustering_icons /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_query_matrices.transfac -from transfac -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/Collection_1_input_motifs_processed_1.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/Collection_1_input_motifs_processed_1.tf -from tf -to transfac -prefix_id Collection_1 -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/Collection_1_input_motifs_processed.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/Collection_1_input_motifs_processed.tf  > /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -split -from tf -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/pairwise_compa.tab'; hclust.method = 'average'; description.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab'; distance.table = '/var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/distance_table.tab'; alignment.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering'; "


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_1_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_2_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_3_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_4_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_5_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_6_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_7_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_8_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_9_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_10_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_11_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_12_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/cluster_13_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_data/cluster_13_transfac_motifs.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m19_assembly_19_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_10/cluster_10_matrices_temp.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m5_assembly_5_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_11/cluster_11_matrices_temp.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m13_assembly_13_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m7_assembly_7_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_cat.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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 'Collection_1:::assembly_19' -set_attr merged_ID 'assembly_19' -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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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 'Collection_1:::assembly_5' -set_attr merged_ID 'assembly_5' -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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_11/cluster_11_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/IC_test_2025-09-16.102227_8CpRiu


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_10/cluster_10_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_11/cluster_11_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m20_assembly_20_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_12/cluster_12_matrices_temp.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m11_assembly_11_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_13/cluster_13_matrices_temp.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m12_assembly_12_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m13_assembly_13_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m7_assembly_7_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_cat.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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 'Collection_1:::assembly_20' -set_attr merged_ID 'assembly_20' -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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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 'Collection_1:::assembly_11' -set_attr merged_ID 'assembly_11' -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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_13/cluster_13_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_13/cluster_13_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_12/cluster_12_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_nb_motifs_3.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/IC_test_2025-09-16.102228_cty94r


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m10_assembly_10_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m1_assembly_1_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m3_assembly_3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m4_assembly_4_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/IC_test_2025-09-16.102229_SUrjhN


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/IC_test_2025-09-16.102229_DmuXqh


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m14_assembly_14_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices_temp.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m15_assembly_15_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m10_assembly_10_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m1_assembly_1_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_2/cluster_2_node_2_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m2_assembly_2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m3_assembly_3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m4_assembly_4_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_2/cluster_3_node_2_cat.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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 'Collection_1:::assembly_14' -set_attr merged_ID 'assembly_14' -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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_2/cluster_2_node_2_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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_2/cluster_2_node_2_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_2/cluster_3_node_2_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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_2/cluster_3_node_2_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_2/cluster_3_nb_motifs_3.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/IC_test_2025-09-16.102230_nY6MRB


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_2/cluster_2_nb_motifs_3.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/IC_test_2025-09-16.102230_DnhbCe


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_2/cluster_2_node_2_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_2/cluster_3_node_2_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m16_assembly_16_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_5/cluster_5_matrices_temp.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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 'Collection_1:::assembly_16' -set_attr merged_ID 'assembly_16' -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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_5/cluster_5_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_5/cluster_5_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m6_assembly_6_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m9_assembly_9_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_6/merged_consensuses/node_1/cluster_6_node_1_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_6/merged_consensuses/node_1/cluster_6_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_6 -name cluster_6 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_6/merged_consensuses/node_1/cluster_6_node_1_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_6/merged_consensuses/node_1/cluster_6_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/IC_test_2025-09-16.102232_xnGtOQ


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_6/merged_consensuses/node_1/cluster_6_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m17_assembly_17_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_7/cluster_7_matrices_temp.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m8_assembly_8_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_8/cluster_8_matrices_temp.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_7/cluster_7_matrices_temp.tf -from tf -to tf  -attr name cluster_7 -attr accession cluster_7 -set_attr merged_AC 'Collection_1:::assembly_17' -set_attr merged_ID 'assembly_17' -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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_7/cluster_7_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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 'Collection_1:::assembly_8' -set_attr merged_ID 'assembly_8' -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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_8/cluster_8_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_8/cluster_8_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_7/cluster_7_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/Collection_1_m18_assembly_18_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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 'Collection_1:::assembly_18' -set_attr merged_ID 'assembly_18' -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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_9/cluster_9_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_clusters_information/cluster_9/cluster_9_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


rm -r /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_portable_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_temporary.html /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/distance_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/alignment_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/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/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/clusters.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/clusters.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/clusters_motif_names.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_tables/clusters_motif_names.html


mv -f /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.102218_UTBNJJ/matrix-clustering_portable_logo_tree.html
