# ========================================================================= # 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 10:41:31 # 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_18.tre -g gene_trees_18.txt -o auto-example-output -f auto-test # # ----------------------------------------------------------------------------------------------------------------------------- # INPUT/OUTPUT INFO: # Species tree file: spec_tree_18.tre # Gene tree file: gene_trees_18.txt # Output directory: auto-example-output # Score file: auto-example-output/auto-test-scores.txt # Filtered gene trees: auto-example-output/auto-test-trees-filtered.txt # Check nums file: auto-example-output/auto-test-checknums.txt # Detailed mapping file: auto-example-output/auto-test-detailed.txt # Duplication count file: auto-example-output/auto-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 auto-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 10:41:31 Reading species tree Success: species tree read 0.40204 0.03565 # 01.22.2025 10:41:31 Parsing hybrid clades Success: got H nodes 0.40708 0.0001 # 01.22.2025 10:41:31 Counting MUL-trees to be generated Success: 133 total MUL-trees 0.41195 9e-05 # 01.22.2025 10:41:31 Building MUL-trees Success: 133 MUL-trees built 0.42785 0.01117 # 01.22.2025 10:41:32 Reading gene trees Success: 1000 gene trees read 0.61268 0.18 # 01.22.2025 10:42:07 Collapsing gene tree groupings Success 35.58205 34.96443 # 01.22.2025 10:42:07 Filtering gene trees over group cap Success: 31 gts over cap 36.44087 0.85382 # WARNING: Gene tree on line 8 is over the group cap in 13 MTs and will be filtered. # WARNING: Gene tree on line 20 is over the group cap in 13 MTs and will be filtered. # WARNING: Gene tree on line 36 is over the group cap in 12 MTs and will be filtered. # WARNING: Gene tree on line 44 is over the group cap in 6 MTs and will be filtered. # WARNING: Gene tree on line 47 is over the group cap in 10 MTs and will be filtered. # WARNING: Gene tree on line 194 is over the group cap in 3 MTs and will be filtered. # WARNING: Gene tree on line 238 is over the group cap in 3 MTs and will be filtered. # WARNING: Gene tree on line 306 is over the group cap in 2 MTs and will be filtered. # WARNING: Gene tree on line 329 is over the group cap in 9 MTs and will be filtered. # WARNING: Gene tree on line 355 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 359 is over the group cap in 4 MTs and will be filtered. # WARNING: Gene tree on line 373 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 376 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 378 is over the group cap in 14 MTs and will be filtered. # WARNING: Gene tree on line 399 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 446 is over the group cap in 14 MTs and will be filtered. # WARNING: Gene tree on line 452 is over the group cap in 22 MTs and will be filtered. # WARNING: Gene tree on line 459 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 518 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 519 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 579 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 616 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 727 is over the group cap in 4 MTs and will be filtered. # WARNING: Gene tree on line 731 is over the group cap in 4 MTs and will be filtered. # WARNING: Gene tree on line 779 is over the group cap in 13 MTs and will be filtered. # WARNING: Gene tree on line 866 is over the group cap in 3 MTs and will be filtered. # WARNING: Gene tree on line 870 is over the group cap in 2 MTs and will be filtered. # WARNING: Gene tree on line 876 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 890 is over the group cap in 3 MTs and will be filtered. # WARNING: Gene tree on line 940 is over the group cap in 1 MTs and will be filtered. # WARNING: Gene tree on line 965 is over the group cap in 3 MTs and will be filtered. # 01.22.2025 10:42:08 INFO: Filtered gene trees: 31 # 01.22.2025 10:42:08 INFO: Final gene tree count for reconciliations: 969 # 01.22.2025 10:42:08 Writing filtered gene trees to file Success: 969 gene trees written 36.61185 0.00912 # ---------------------------------------- # 01.22.2025 10:44:38 Reconciliation Success 187.33412 150.71252 # 01.22.2025 10:44:46 Getting maps for lowest scoring MTs Success 195.07796 7.73829 # 01.22.2025 10:44:46 Writing detailed output file Success 195.09754 0.01454 # 01.22.2025 10:44:46 Writing main output file Success 195.12981 0.02752 # =============================================================================================================================================================================== # # Done! # The date and time at the end is: 01.22.2025 10:44:46 # Total execution time: 195.145 seconds. # Output directory for this run: auto-example-output # Log file for this run: auto-example-output/auto-test.log # GRAMPA finished with 31 WARNINGS -- check log file for more info # ---------------------------------------- # The MUL-tree with the minimum parsimony score is MT-119: (((B,A)<1>,((((x+,y+)<2>,z+)<3>,((x*,y*)<4>,z*)<5>)<6>,C)<7>)<8>,D)<9> # Score = 4807 # ---------------------------------------- # =============================================================================================================================================================================== #