rsync -ruptl /var/www/html/rsat/perl-scripts/lib/js /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY
rsync -ruptl /var/www/html/rsat/public_html/images/program_icons/matrix-clustering_icons /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_query_matrices.transfac -from tf -to tf -perm 1 -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data/oct4_peak_motifs_random_motifs.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data/oct4_peak_motifs_random_motifs.tf -from transfac -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed_1.tf
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed_1.tf -from tf -to transfac -prefix_id oct4_peak_motifs -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed.tf
cat /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed.tf > /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/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/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data/input_motifs_processed.tf -split -from tf -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/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/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/pairwise_compa.tab'; hclust.method = 'average'; description.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab'; distance.table = '/var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/distance_table.tab'; alignment.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/alignment_table.tab'; verbosity = 0; metric = 'Ncor'; heatmap.color.palette = 'YlOrRd'; heatmap.color.classes = '9'; export.newick = 0; radial.only = 1; 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/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering'; "
/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/cluster_1_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data/cluster_1_transfac_motifs.tf
rm -r /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_pairwise_compa_logos
/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/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/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/distance_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/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/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/alignment_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/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/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/clusters.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/clusters.html
/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/clusters_motif_names.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/clusters_motif_names.html
; matrix-clustering -v 1 -max_matrices 300 -matrix oct4_peak_motifs $RSAT/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_query_matrices.transfac transfac -hclust_method average -calc sum -title oct4_motifs_found_in_chen_2008_peak_sets -metric_build_tree Ncor -lth w 5 -lth cor 0.6 -lth Ncor 0.4 -quick -rand -radial_tree_only -label_in_tree name -return json,heatmap -o $RSAT/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering
; Program version 1.05
; Number of matrices 22
; Output files
; alignment_table /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/alignment_table.tab
; pairwise_compa_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_html/pairwise_compa.html
; motif_richness_barplot_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_motif_richness_barplot.html
; summary /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_SUMMARY.html
; summary_temp /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_SUMMARY_TEMP.html
; clusters_table_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/clusters.html
; root_motifs /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_cluster_root_motifs.tf
; Rlog /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_Rlog.txt
; archive /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_archive.zip
; clusters_table_motif_names_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/clusters_motif_names.html
; consensus_cladogram_json /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_trees/tree.json
; heatmap_coverage_d3 /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/convergency_heatmap_tab.tsv
; internal_nodes_attributes_table /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/internal_nodes_attributes.tab
; temp_html_2 /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_temporary_2.html
; matrix_descriptions_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_html/pairwise_compa_matrix_descriptions.html
; dynamic_coverage_heatmap_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_dynamic_coverage_heatmap.html
; logo_cladogram_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_logo_tree.html
; radial_tree /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_radial_tree.html
; ref_collection_tf /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_reference_collection.tf
; nb_clusters_table /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/number_of_clusters.tab
; matrix_descriptions /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab
; reference_compa /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/Root_vs_reference_collection_compa.tab
; small_logo_cladogram_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_portable_logo_tree.html
; clusters_table_motif_names /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/clusters_motif_names.tab
; heatmap_collections_d3 /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/collection_heatmap_tab.tsv
; distance_table /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/distance_table.tab
; cluster_summary_table /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/clusters_summary_table.tab
; coverage_json_folder /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_coverage_json
; cluster_IDs_names /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_cluster_IDs.txt
; motif_file /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data/input_motifs_processed.tf
; hexa_colors /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_hexa_colors.txt
; central_motifs_tf /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_central_motifs_transfac.tf
; alignment_table_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/alignment_table.html
; temp_html_3 /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_temporary_3.html
; distance_table_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/distance_table.html
; log /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_log.txt
; input_matrices /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data/input_motifs_processed.tf
; html_index /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_html/index.html
; radial_tree_template /var/www/html/rsat/public_html/templates_html/Radial_tree_template.html
; int_align /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/intermediate_alignments.tab
; central_motifs /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_central_motifs_IDs.tab
; heatmap_pdf /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_figures/heatmap.pdf
; clusters_table /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/clusters.tab
; err_log /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_errors.txt
; percent_table /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/clusters_summary_percent_table.tab
; all_concatenated_motifs /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_aligned_logos/All_concatenated_motifs.tf
; heatmap_coverage_attributes /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/convergency_heatmap_attributes.tab
; dynamic_heatmap_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_dynamic_heatmap.html
; prefix /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering
; small_forest_export /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_small_forest.html
; heatmap_jpg /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_figures/heatmap.jpg
; temp_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_temporary.html
; pairwise_compa /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/pairwise_compa.tab
; motif_richness_tsv /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_motif_richness.tsv
; coverage_table /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/clusters_summary_coverage_contingency_table.tab
; root_motifs_table /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_root_motifs_table.tab
; central_motifs_IDs_temp /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_central_motifs_IDs_temporal.tab
; reference_compa_html /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_html/Root_vs_reference_collection_compa.html
; heatmap_collections_attributes /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_tables/collection_heatmap_order.tab
; Directories
; data /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY/matrix-clustering_data
; output /var/www/html/rsat/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.223844_iK1RsY
; Host name rsat
; Job started 2025-03-04.223844
; Job done 2025-03-04.223853
; Seconds 0.45
; user 0.45
; system 0.17
; cuser 12.04
; csystem 2.23