# ========================================================================= # Welcome to GRAMPA -- Gene tree reconciliations with MUL-trees. # Version 1.4.0 released on March 2023 # GRAMPA was developed by Gregg Thomas, S. Hussain Ather, Matthew Hahn # Citation: https://doi.org/10.1093/sysbio/syx044 # Website: https://gwct.github.io/grampa/ # Report issues: https://github.com/gwct/grampa # # The date and time at the start is: 01.22.2025 10:58:14 # Using Python executable located at: /n/home07/gthomas/miniconda3/envs/grampa-issue8-1/bin/python3.13 # Using Python version: 3.13.1 # # The program was called as: /n/home07/gthomas/miniconda3/envs/grampa-issue8-1/bin/grampa -s spec_tree_3a.tre -g gene_trees_3a.txt -h1 x 1 2 -h2 C D 5 6 -o ex2-output -f ex2-test # # ----------------------------------------------------------------------------------------------------------------------------- # INPUT/OUTPUT INFO: # Species tree file: spec_tree_3a.tre # Gene tree file: gene_trees_3a.txt # Output directory: ex2-output # Score file: ex2-output/ex2-test-scores.txt # Filtered gene trees: ex2-output/ex2-test-trees-filtered.txt # Check nums file: ex2-output/ex2-test-checknums.txt # Detailed mapping file: ex2-output/ex2-test-detailed.txt # Duplication count file: ex2-output/ex2-test-dup-counts.txt # ----------------------------------------------------------------------------------------------------------------------------- # OPTIONS INFO: # Option Current setting Current action # -h1 x 1 2 GRAMPA will search these H1 nodes. If none are specified, all nodes will be searched as H1 nodes. # -h2 C D 5 6 GRAMPA will search these H2 nodes. If none are specified, all nodes will be searched as H2 nodes. # -c 8 Gene trees with more than this number of groups/clades with polyploid species for a given h1/h2 combination will be skipped. # -f ex2-test All output files generated will have this string preprended to them. # -p 1 GRAMPA will use this number of processes for LCA mapping. # -v 3 Controls the amount of info printed to the screen as GRAMPA is running. # --multree False The tree input with -s will be read as singly-labeled tree. # --checknums False GRAMPA will count groups to filter gene trees and then perform reconciliations. # --no-st, --st-only default GRAMPA will perform reconciliations to all MUL-trees specified by -h1 and -h2 and the input species tree. # --maps False GRAMPA will only output duplication and loss counts in the detailed output file. # ------------------------------------------------------------------------------------------------------------------------------------------------------ # Date Time Current step Status Elapsed time (s) Step time (s) # ------------------------------------------------------------------------------------------------------------------------------------------------------ # 01.22.2025 10:58:14 Reading species tree Success: species tree read 0.38206 0.01976 # 01.22.2025 10:58:14 Parsing hybrid clades Success: got H nodes 0.38694 9e-05 # 01.22.2025 10:58:14 Counting MUL-trees to be generated Success: 12 total MUL-trees 0.39173 4e-05 # 01.22.2025 10:58:14 Building MUL-trees Success: 12 MUL-trees built 0.39819 0.00156 # 01.22.2025 10:58:14 Reading gene trees Success: 1000 gene trees read 0.59834 0.19537 # 01.22.2025 10:58:17 Collapsing gene tree groupings Success 3.69892 3.0957 # 01.22.2025 10:58:17 Filtering gene trees over group cap Success: 0 gts over cap 3.79293 0.08927 # 01.22.2025 10:58:17 INFO: No trees filtered! Using your original set. # ---------------------------------------- # 01.22.2025 10:58:32 Reconciliation Success 18.34007 14.53308 # 01.22.2025 10:58:42 Getting maps for lowest scoring MTs Success 27.92074 9.57533 # 01.22.2025 10:58:42 Writing detailed output file Success 27.93531 0.00953 # 01.22.2025 10:58:42 Writing main output file Success 27.97084 0.03046 # =============================================================================================================================================================================== # # Done! # The date and time at the end is: 01.22.2025 10:58:42 # Total execution time: 27.983 seconds. # Output directory for this run: ex2-output # Log file for this run: ex2-output/ex2-test.log # ---------------------------------------- # The MUL-tree with the minimum parsimony score is MT-9: ((((((x+,y+)<1>,z+)<2>,B)<3>,A)<4>,(C,((x*,y*)<5>,z*)<6>)<7>)<8>,D)<9> # Score = 5242 # ---------------------------------------- # =============================================================================================================================================================================== #