RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 18-Jul-2021 10:04:24 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5SZD4/2_msa/Q5SZD4_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5SZD4/3_mltree/Q5SZD4 --seed 2 --threads 6 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5SZD4/2_msa/Q5SZD4_trimmed_msa.fasta [00:00:00] Loaded alignment with 303 taxa and 275 sites WARNING: Sequences tr_A0A2J8LCH7_A0A2J8LCH7_PANTR_9598 and sp_Q6IB77_GLYAT_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q3Q5_H2Q3Q5_PANTR_9598 and tr_A0A2R9B276_A0A2R9B276_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7HA37_F7HA37_MACMU_9544 and tr_G7PS78_G7PS78_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2K6CN34_A0A2K6CN34_MACNE_9545 and tr_A0A2K5YQX5_A0A2K5YQX5_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 4 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5SZD4/3_mltree/Q5SZD4.raxml.reduced.phy Alignment comprises 1 partitions and 275 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 275 / 275 Gaps: 8.08 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5SZD4/3_mltree/Q5SZD4.raxml.rba Parallelization scheme autoconfig: 6 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 303 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 275 / 22000 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -152202.965761] Initial branch length optimization [00:00:01 -125868.932229] Model parameter optimization (eps = 10.000000) [00:00:22 -125163.971550] AUTODETECT spr round 1 (radius: 5) [00:00:48 -87084.274893] AUTODETECT spr round 2 (radius: 10) [00:01:24 -66208.396970] AUTODETECT spr round 3 (radius: 15) [00:02:06 -61895.103534] AUTODETECT spr round 4 (radius: 20) [00:03:01 -61561.812570] AUTODETECT spr round 5 (radius: 25) [00:03:58 -61535.082388] SPR radius for FAST iterations: 25 (autodetect) [00:03:58 -61535.082388] Model parameter optimization (eps = 3.000000) [00:04:14 -61250.812127] FAST spr round 1 (radius: 25) [00:04:47 -57161.106540] FAST spr round 2 (radius: 25) [00:05:15 -56848.784952] FAST spr round 3 (radius: 25) [00:05:40 -56829.537165] FAST spr round 4 (radius: 25) [00:06:00 -56828.591608] FAST spr round 5 (radius: 25) [00:06:19 -56828.579286] Model parameter optimization (eps = 1.000000) [00:06:26 -56825.964316] SLOW spr round 1 (radius: 5) [00:07:10 -56811.239022] SLOW spr round 2 (radius: 5) [00:07:47 -56809.879987] SLOW spr round 3 (radius: 5) [00:08:24 -56805.700677] SLOW spr round 4 (radius: 5) [00:08:58 -56805.688746] SLOW spr round 5 (radius: 10) [00:09:40 -56805.687260] SLOW spr round 6 (radius: 15) [00:11:04 -56805.685770] SLOW spr round 7 (radius: 20) [00:12:39 -56805.684278] SLOW spr round 8 (radius: 25) [00:13:07] [worker #1] ML tree search #2, logLikelihood: -56807.543810 [00:13:42] [worker #5] ML tree search #6, logLikelihood: -56799.936583 [00:13:52] [worker #2] ML tree search #3, logLikelihood: -56803.798741 [00:14:05 -56805.682783] Model parameter optimization (eps = 0.100000) [00:14:09] [worker #0] ML tree search #1, logLikelihood: -56805.624406 [00:14:09 -152643.720192] Initial branch length optimization [00:14:10 -126221.889966] Model parameter optimization (eps = 10.000000) [00:14:22] [worker #4] ML tree search #5, logLikelihood: -56800.569061 [00:14:35 -125571.511178] AUTODETECT spr round 1 (radius: 5) [00:15:01 -90600.814154] AUTODETECT spr round 2 (radius: 10) [00:15:38 -70965.400525] AUTODETECT spr round 3 (radius: 15) [00:15:45] [worker #3] ML tree search #4, logLikelihood: -56802.707548 [00:16:31 -62198.410893] AUTODETECT spr round 4 (radius: 20) [00:17:21 -61904.274119] AUTODETECT spr round 5 (radius: 25) [00:18:00 -61670.173263] SPR radius for FAST iterations: 25 (autodetect) [00:18:00 -61670.173263] Model parameter optimization (eps = 3.000000) [00:18:17 -61423.284595] FAST spr round 1 (radius: 25) [00:18:52 -57038.760458] FAST spr round 2 (radius: 25) [00:19:21 -56886.325876] FAST spr round 3 (radius: 25) [00:19:46 -56864.919839] FAST spr round 4 (radius: 25) [00:20:08 -56826.165147] FAST spr round 5 (radius: 25) [00:20:28 -56822.763558] FAST spr round 6 (radius: 25) [00:20:47 -56822.761984] Model parameter optimization (eps = 1.000000) [00:20:57 -56813.103228] SLOW spr round 1 (radius: 5) [00:21:38 -56801.645067] SLOW spr round 2 (radius: 5) [00:22:14 -56801.196448] SLOW spr round 3 (radius: 5) [00:22:49 -56801.195198] SLOW spr round 4 (radius: 10) [00:23:29 -56801.195036] SLOW spr round 5 (radius: 15) [00:24:52 -56801.195011] SLOW spr round 6 (radius: 20) [00:26:25 -56801.195008] SLOW spr round 7 (radius: 25) [00:27:35] [worker #1] ML tree search #8, logLikelihood: -56803.313481 [00:27:39] [worker #2] ML tree search #9, logLikelihood: -56800.261095 [00:27:52 -56801.195007] Model parameter optimization (eps = 0.100000) [00:27:56] [worker #5] ML tree search #12, logLikelihood: -56802.023526 [00:27:56] [worker #0] ML tree search #7, logLikelihood: -56801.090943 [00:27:56 -153896.956892] Initial branch length optimization [00:27:58 -127645.096602] Model parameter optimization (eps = 10.000000) [00:28:20 -127113.773615] AUTODETECT spr round 1 (radius: 5) [00:28:40] [worker #3] ML tree search #10, logLikelihood: -56803.887669 [00:28:46 -92540.465686] AUTODETECT spr round 2 (radius: 10) [00:29:22 -72084.728170] AUTODETECT spr round 3 (radius: 15) [00:30:08 -63712.932724] AUTODETECT spr round 4 (radius: 20) [00:30:17] [worker #4] ML tree search #11, logLikelihood: -56801.749276 [00:31:02 -63428.262553] AUTODETECT spr round 5 (radius: 25) [00:31:57 -63394.561060] SPR radius for FAST iterations: 25 (autodetect) [00:31:57 -63394.561060] Model parameter optimization (eps = 3.000000) [00:32:11 -63187.986737] FAST spr round 1 (radius: 25) [00:32:49 -57246.026059] FAST spr round 2 (radius: 25) [00:33:21 -56835.808154] FAST spr round 3 (radius: 25) [00:33:43 -56820.168271] FAST spr round 4 (radius: 25) [00:34:03 -56817.692264] FAST spr round 5 (radius: 25) [00:34:22 -56817.654398] Model parameter optimization (eps = 1.000000) [00:34:30 -56815.004789] SLOW spr round 1 (radius: 5) [00:35:12 -56804.028075] SLOW spr round 2 (radius: 5) [00:35:51 -56802.855223] SLOW spr round 3 (radius: 5) [00:36:26 -56802.830737] SLOW spr round 4 (radius: 10) [00:37:07 -56802.051975] SLOW spr round 5 (radius: 5) [00:38:03 -56801.821080] SLOW spr round 6 (radius: 5) [00:38:48 -56801.820348] SLOW spr round 7 (radius: 10) [00:39:32 -56801.820164] SLOW spr round 8 (radius: 15) [00:40:53 -56801.820105] SLOW spr round 9 (radius: 20) [00:41:39] [worker #5] ML tree search #18, logLikelihood: -56806.079259 [00:42:02] [worker #1] ML tree search #14, logLikelihood: -56799.986756 [00:42:25 -56801.820085] SLOW spr round 10 (radius: 25) [00:42:55] [worker #2] ML tree search #15, logLikelihood: -56798.378915 [00:42:57] [worker #3] ML tree search #16, logLikelihood: -56801.435400 [00:43:51 -56801.820079] Model parameter optimization (eps = 0.100000) [00:43:53] [worker #0] ML tree search #13, logLikelihood: -56801.752949 [00:43:53 -151900.370368] Initial branch length optimization [00:43:55 -126208.549140] Model parameter optimization (eps = 10.000000) [00:44:12 -125645.833180] AUTODETECT spr round 1 (radius: 5) [00:44:39 -90515.285500] AUTODETECT spr round 2 (radius: 10) [00:45:13 -69856.772148] AUTODETECT spr round 3 (radius: 15) [00:45:54 -63574.637732] AUTODETECT spr round 4 (radius: 20) [00:46:21] [worker #4] ML tree search #17, logLikelihood: -56801.610029 [00:46:42 -62107.138796] AUTODETECT spr round 5 (radius: 25) [00:47:36 -62103.053350] SPR radius for FAST iterations: 25 (autodetect) [00:47:36 -62103.053350] Model parameter optimization (eps = 3.000000) [00:47:51 -61885.002267] FAST spr round 1 (radius: 25) [00:48:26 -57106.738332] FAST spr round 2 (radius: 25) [00:48:57 -56848.211545] FAST spr round 3 (radius: 25) [00:49:21 -56830.653091] FAST spr round 4 (radius: 25) [00:49:40 -56830.627363] Model parameter optimization (eps = 1.000000) [00:49:48 -56816.438555] SLOW spr round 1 (radius: 5) [00:50:32 -56803.784414] SLOW spr round 2 (radius: 5) [00:51:07 -56803.309654] SLOW spr round 3 (radius: 5) [00:51:42 -56803.295104] SLOW spr round 4 (radius: 10) [00:52:22 -56803.292482] SLOW spr round 5 (radius: 15) [00:53:47 -56803.292434] SLOW spr round 6 (radius: 20) [00:54:59] [worker #1] ML tree search #20, logLikelihood: -56816.871919 [00:55:26 -56803.292434] SLOW spr round 7 (radius: 25) [00:56:48 -56803.292434] Model parameter optimization (eps = 0.100000) [00:56:51] [worker #0] ML tree search #19, logLikelihood: -56803.221534 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.212458,0.738089) (0.118307,0.704929) (0.428343,0.929259) (0.240892,1.501698) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Final LogLikelihood: -56798.378915 AIC score: 114814.757831 / AICc score: 857794.757831 / BIC score: 117017.371429 Free parameters (model + branch lengths): 609 WARNING: Number of free parameters (K=609) is larger than alignment size (n=275). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5SZD4/3_mltree/Q5SZD4.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5SZD4/3_mltree/Q5SZD4.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5SZD4/3_mltree/Q5SZD4.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5SZD4/3_mltree/Q5SZD4.raxml.log Analysis started: 18-Jul-2021 10:04:24 / finished: 18-Jul-2021 11:01:16 Elapsed time: 3411.868 seconds