INFO Selected: Output dir: /Users/melodymale/McrA_output/intermediates/place/
INFO Selected: Query file: /Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group0_queries.mfa
INFO Selected: Tree file: /Users/melodymale/McrA_output/intermediates/McrA_RefPkg/0423.1619159847/McrA.nwk
INFO Selected: Reference MSA: /Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group0_references.mfa
INFO Selected: Filtering by minimum threshold: 0.01
INFO Selected: Prescoring by accumulated LWR threshold: 0.9
INFO Selected: Disabling pre-masking. (repeats enabled!)
INFO Selected: Automatic switching of use of per rate scalers
INFO Selected: Preserving the root of the input tree
INFO Selected: Specified model file: /Users/melodymale/McrA_output/intermediates/McrA_RefPkg/0423.1619159847/McrA_epa.model
INFO Selected: Using threads: 4
INFO     ______ ____   ___           _   __ ______
        / ____// __ \ /   |         / | / // ____/
       / __/  / /_/ // /| | ______ /  |/ // / __  
      / /___ / ____// ___ |/_____// /|  // /_/ /  
     /_____//_/    /_/  |_|      /_/ |_/ \____/ (v0.3.8)
INFO Using model parameters:
INFO    Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 1.09629 (user),  weights&rates: (0.25,0.155755) (0.25,0.503896) (0.25,1.01429) (0.25,2.32606) 
        Base frequencies (model): 0.079066 0.055941 0.041977 0.053052 0.012937 0.040767 0.071586 0.057337 0.022355 0.062157 0.099081 0.0646 0.022951 0.042302 0.04404 0.061197 0.053287 0.012066 0.034155 0.069147 
        Substitution rates (model): 0.425093 0.276818 0.395144 2.48908 0.969894 1.03855 2.06604 0.358858 0.14983 0.395337 0.536518 1.12403 0.253701 1.17765 4.72718 2.1395 0.180717 0.218959 2.54787 0.751878 0.123954 0.534551 2.80791 0.36397 0.390192 2.4266 0.126991 0.301848 6.32607 0.484133 0.052722 0.332533 0.858151 0.578987 0.593607 0.31444 0.170887 5.07615 0.528768 1.69575 0.541712 1.43765 4.50924 0.191503 0.068427 2.14508 0.371004 0.089525 0.161787 4.00836 2.00068 0.045376 0.612025 0.083688 0.062556 0.523386 5.24387 0.844926 0.927114 0.01069 0.015076 0.282959 0.025548 0.017416 0.394456 1.24028 0.42586 0.02989 0.135107 0.037967 0.084808 0.003499 0.569265 0.640543 0.320627 0.594007 0.013266 0.89368 1.10525 0.075382 2.78448 1.14348 0.670128 1.16553 1.95929 4.12859 0.267959 4.81351 0.072854 0.582457 3.23429 1.67257 0.035855 0.624294 1.22383 1.08014 0.236199 0.257336 0.210332 0.348847 0.423881 0.044265 0.069673 1.80718 0.173735 0.018811 0.419409 0.611973 0.604545 0.077852 0.120037 0.245034 0.311484 0.008705 0.044261 0.296636 0.139538 0.089586 0.196961 1.73999 0.129836 0.268491 0.054679 0.076701 0.108882 0.366317 0.697264 0.442472 0.682139 0.508851 0.990012 0.584262 0.597054 5.30683 0.119013 4.14507 0.159069 4.27361 1.11273 0.078281 0.064105 1.03374 0.11166 0.232523 10.6491 0.1375 6.31236 2.59269 0.24906 0.182287 0.302936 0.619632 0.299648 1.70274 0.656604 0.023918 0.390322 0.748683 1.13686 0.049906 0.131932 0.185202 1.79885 0.099849 0.34696 2.02037 0.696175 0.481306 1.89872 0.094464 0.361819 0.165001 2.45712 7.8039 0.654683 1.33813 0.571468 0.095131 0.089613 0.296501 6.47228 0.248862 0.400547 0.098369 0.140825 0.245841 2.18816 3.15182 0.18951 0.249313
INFO Output file: /Users/melodymale/McrA_output/intermediates/place/epa_result.jplace