diff test-data/test2_logs.txt @ 4:e64af72e1b8f draft default tip

planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_clusters_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2_logs.txt	Mon Dec 15 16:44:40 2025 +0000
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+=== CD-HIT cluster processing started ===
+cluster_file: provided
+annotation_file: provided
+=== PARAMETERS ===
+output_taxa_clusters: True
+output_taxa_processed: True
+simi_plot_y_min: 95.0
+simi_plot_y_max: 100.0
+uncertain_taxa_use_ratio: 0.5
+min_to_split: 0.45
+min_count_to_split: 10
+min_cluster_support: 1
+=== PARAMETERS END===
+Loaded 622 annotated headers
+Parsed 268 clusters
+Similarity text summary written succesfully
+Similarity mean = 99.80, std = 0.50
+Similarity plot written succesfully
+Count summary written succesfully
+TOTAL annotated=49571, unannotated=16561, total=66132
+Raw taxa per cluster written succesfully
+Processed taxa (split clusters) written succesfully
+=== SUMMARY ===
+Clusters parsed: 268
+Total reads: 66132
+Annotated reads: 49571
+Unannotated reads: 16561
+Clusters with annotations: 29
+Clusters fully unannotated: 239
+Minimum cluster support for processed taxa: 1
+=== TAXA SUMMARY (top 10) ===
+Viridiplantae / Streptophyta / Magnoliopsida / Rosales / Cannabaceae / Humulus / Humulus lupulus: 47123 reads
+Viridiplantae / Streptophyta / Magnoliopsida / Rosales / Rosaceae / Uncertain taxa / Uncertain taxa: 383 reads
+Viridiplantae / Streptophyta / Magnoliopsida / Fagales / Betulaceae / Alnus / Alnus incana: 300 reads
+Viridiplantae / Streptophyta / Magnoliopsida / Poales / Poaceae / Uncertain taxa / Uncertain taxa: 288 reads
+Viridiplantae / Streptophyta / Magnoliopsida / Malpighiales / Salicaceae / Populus / Uncertain taxa: 224 reads
+Viridiplantae / Streptophyta / Magnoliopsida / Fagales / Fagaceae / Quercus / Quercus rubra: 202 reads
+Viridiplantae / Streptophyta / Magnoliopsida / Solanales / Uncertain taxa / Uncertain taxa / Uncertain taxa: 180 reads
+Viridiplantae / Streptophyta / Magnoliopsida / Gentianales / Rubiaceae / Uncertain taxa / Uncertain taxa: 156 reads
+Viridiplantae / Streptophyta / Magnoliopsida / Uncertain taxa / Uncertain taxa / Uncertain taxa / Uncertain taxa: 146 reads
+Viridiplantae / Streptophyta / Magnoliopsida / Caryophyllales / Polygonaceae / Uncertain taxa / Uncertain taxa: 134 reads
+Total unique taxa: 22
+=== SIMILARITY SUMMARY ===
+Mean similarity: 99.80
+Std similarity: 0.50
+=== CD-HIT cluster processing finished ===
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