# ========================================================================= # 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 10:34:49 # 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 -o allo-example-output -f allo-test -v 0 # # ----------------------------------------------------------------------------------------------------------------------------- # INPUT/OUTPUT INFO: # Species tree file: spec_tree_3a.tre # Gene tree file: gene_trees_3a.txt # Output directory: allo-example-output # Score file: allo-example-output/allo-test-scores.txt # Filtered gene trees: allo-example-output/allo-test-trees-filtered.txt # Check nums file: allo-example-output/allo-test-checknums.txt # Detailed mapping file: allo-example-output/allo-test-detailed.txt # Duplication count file: allo-example-output/allo-test-dup-counts.txt # ----------------------------------------------------------------------------------------------------------------------------- # OPTIONS INFO: # Option Current setting Current action # -h1 All GRAMPA will search these H1 nodes. If none are specified, all nodes will be searched as H1 nodes. # -h2 All 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 allo-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 0 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 10:34:49 Reading species tree Success: species tree read 0.36815 0.00307 # 01.22.2025 10:34:49 Parsing hybrid clades Success: got H nodes 0.37295 0.00011 # 01.22.2025 10:34:49 Counting MUL-trees to be generated Success: 127 total MUL-trees 0.37772 8e-05 # 01.22.2025 10:34:49 Building MUL-trees Success: 127 MUL-trees built 0.39328 0.01081 # 01.22.2025 10:34:49 Reading gene trees Success: 1000 gene trees read 0.55544 0.15745 # 01.22.2025 10:35:21 Collapsing gene tree groupings Success 32.34832 31.78778 # 01.22.2025 10:35:22 Filtering gene trees over group cap Success: 13 gts over cap 33.1695 0.81608 # WARNING: Gene tree on line 177 is over the group cap in 5 MTs and will be filtered. # WARNING: Gene tree on line 263 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 350 is over the group cap in 2 MTs and will be filtered. # WARNING: Gene tree on line 525 is over the group cap in 2 MTs and will be filtered. # WARNING: Gene tree on line 562 is over the group cap in 5 MTs and will be filtered. # WARNING: Gene tree on line 581 is over the group cap in 10 MTs and will be filtered. # WARNING: Gene tree on line 635 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 664 is over the group cap in 2 MTs and will be filtered. # WARNING: Gene tree on line 747 is over the group cap in 2 MTs and will be filtered. # WARNING: Gene tree on line 765 is over the group cap in 13 MTs and will be filtered. # WARNING: Gene tree on line 785 is over the group cap in 3 MTs and will be filtered. # WARNING: Gene tree on line 877 is over the group cap in 2 MTs and will be filtered. # WARNING: Gene tree on line 903 is over the group cap in 2 MTs and will be filtered. # 01.22.2025 10:35:22 INFO: Filtered gene trees: 13 # 01.22.2025 10:35:22 INFO: Final gene tree count for reconciliations: 987 # 01.22.2025 10:35:22 Writing filtered gene trees to file Success: 987 gene trees written 33.25487 0.00916 # ---------------------------------------- # 01.22.2025 10:37:24 Reconciliation Success 155.64531 122.38106 # 01.22.2025 10:37:32 Getting maps for lowest scoring MTs Success 163.06909 7.41838 # 01.22.2025 10:37:32 Writing detailed output file Success 163.08659 0.01233 # 01.22.2025 10:37:32 Writing main output file Success 163.12056 0.02928 # =============================================================================================================================================================================== # # Done! # The date and time at the end is: 01.22.2025 10:37:32 # Total execution time: 163.132 seconds. # Output directory for this run: allo-example-output # Log file for this run: allo-example-output/allo-test.log # GRAMPA finished with 13 WARNINGS -- check log file for more info # ---------------------------------------- # The MUL-tree with the minimum parsimony score is MT-105: ((((((x+,y+)<1>,z+)<2>,B)<3>,A)<4>,(C,((x*,y*)<5>,z*)<6>)<7>)<8>,D)<9> # Score = 5018 # ---------------------------------------- # =============================================================================================================================================================================== #