# =========================================================================
# 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  11:24:30
# 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:          ../../../grampa.py -s mul_tree_74_3a.tre -g gene_trees_3a.txt -o ex3-output -f count-test --multree --overwrite
#
# -----------------------------------------------------------------------------------------------------------------------------
# INPUT/OUTPUT INFO:
# Species tree file:                    mul_tree_74_3a.tre
# Gene tree file:                       gene_trees_3a.txt
# Output directory:                     ex3-output
# Score file:                           ex3-output/count-test-scores.txt
# Filtered gene trees:                  ex3-output/count-test-trees-filtered.txt
# Check nums file:                      ex3-output/count-test-checknums.txt
# Detailed mapping file:                ex3-output/count-test-detailed.txt
# Duplication count file:               ex3-output/count-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                                    count-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                             True                          The tree input with -s will be read as a MUL-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  11:24:31  Reading species tree                              Success: species tree read              0.36131             0.00364         
# 01.22.2025  11:24:31  Parsing hybrid clades                             Success: got H nodes                    0.36617             8e-05           
# 01.22.2025  11:24:31  Counting MUL-trees to be generated                Success: 1 total MUL-trees              0.37091             3e-05           
# 01.22.2025  11:24:31  Reading gene trees                                Success: 1000 gene trees read           0.52038             0.14474         
# 01.22.2025  11:24:31  Collapsing gene tree groupings                    Success                                 0.71792             0.19255         
# 01.22.2025  11:24:31  Filtering gene trees over group cap               Success: 0 gts over cap                 0.73735             0.01452         
# 01.22.2025  11:24:31  INFO: No trees filtered! Using your original set.
# ----------------------------------------
# 01.22.2025  11:24:33  Reconciliation                                    Success                                 2.18713             1.43517         
# 01.22.2025  11:24:34  Getting maps for lowest scoring MTs               Success                                 3.63161             1.43944         
# 01.22.2025  11:24:34  Writing detailed output file                      Success                                 3.64582             0.0091          
# 01.22.2025  11:24:34  Writing main output file                          Success                                 3.66868             0.01819         
# ===============================================================================================================================================================================
#
# Done!
# The date and time at the end is: 01.22.2025  11:24:34
# Total execution time:            3.674 seconds.
# Output directory for this run:   ex3-output
# Log file for this run:           ex3-output/count-test.log
# ----------------------------------------
# ===============================================================================================================================================================================
#