# ========================================================================= # 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 10:49:33 # 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_33.tre -g gene_trees_33.txt -o nop-example-output -f nop-test # # ----------------------------------------------------------------------------------------------------------------------------- # INPUT/OUTPUT INFO: # Species tree file: spec_tree_33.tre # Gene tree file: gene_trees_33.txt # Output directory: nop-example-output # Score file: nop-example-output/nop-test-scores.txt # Filtered gene trees: nop-example-output/nop-test-trees-filtered.txt # Check nums file: nop-example-output/nop-test-checknums.txt # Detailed mapping file: nop-example-output/nop-test-detailed.txt # Duplication count file: nop-example-output/nop-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 nop-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 10:49:33 Reading species tree Success: species tree read 0.37986 0.01698 # 01.22.2025 10:49:33 Parsing hybrid clades Success: got H nodes 0.38475 0.00011 # 01.22.2025 10:49:33 Counting MUL-trees to be generated Success: 127 total MUL-trees 0.38962 0.0001 # 01.22.2025 10:49:33 Building MUL-trees Success: 127 MUL-trees built 0.40488 0.01048 # 01.22.2025 10:49:33 Reading gene trees Success: 1000 gene trees read 0.53361 0.12395 # 01.22.2025 10:49:58 Collapsing gene tree groupings Success 24.6194 24.08071 # 01.22.2025 10:49:58 Filtering gene trees over group cap Success: 1 gts over cap 25.41411 0.78963 # WARNING: Gene tree on line 898 is over the group cap in 2 MTs and will be filtered. # 01.22.2025 10:49:58 INFO: Filtered gene trees: 1 # 01.22.2025 10:49:58 INFO: Final gene tree count for reconciliations: 999 # 01.22.2025 10:49:58 Writing filtered gene trees to file Success: 999 gene trees written 25.44174 0.00879 # ---------------------------------------- # 01.22.2025 10:50:53 Reconciliation Success 79.61308 54.16214 # 01.22.2025 10:50:56 Getting maps for lowest scoring MTs Success 82.59075 2.97224 # 01.22.2025 10:50:56 Writing detailed output file Success 82.60493 0.00915 # 01.22.2025 10:50:56 Writing main output file Success 82.63672 0.02714 # =============================================================================================================================================================================== # # Done! # The date and time at the end is: 01.22.2025 10:50:56 # Total execution time: 82.65 seconds. # Output directory for this run: nop-example-output # Log file for this run: nop-example-output/nop-test.log # GRAMPA finished with 1 WARNINGS -- check log file for more info # ---------------------------------------- # The tree with the minimum parsimony score is the singly-labled tree (ST): ((((((x:1,y:1):1,z:2):1,B:3):1,A:4):1,C:5):1,D:6) # Score = 4115 # ---------------------------------------- # =============================================================================================================================================================================== #