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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM RAxML-NG was called at 26-Jul-2021 00:10:22 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8MTL3/2_msa/A8MTL3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8MTL3/3_mltree/A8MTL3 --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: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8MTL3/2_msa/A8MTL3_trimmed_msa.fasta [00:00:00] Loaded alignment with 126 taxa and 279 sites WARNING: Sequences tr_A0A2J8QK70_A0A2J8QK70_PANTR_9598 and tr_A0A2R9AD57_A0A2R9AD57_PANPA_9597 are exactly identical! WARNING: Sequences tr_G7P9V5_G7P9V5_MACFA_9541 and tr_A0A2K6C4K7_A0A2K6C4K7_MACNE_9545 are exactly identical! WARNING: Duplicate sequences found: 2 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8MTL3/3_mltree/A8MTL3.raxml.reduced.phy Alignment comprises 1 partitions and 278 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 279 / 278 Gaps: 22.82 % Invariant sites: 0.36 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8MTL3/3_mltree/A8MTL3.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 126 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 278 / 22240 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -53716.166037] Initial branch length optimization [00:00:00 -41282.210824] Model parameter optimization (eps = 10.000000) [00:00:17 -41075.373463] AUTODETECT spr round 1 (radius: 5) [00:00:29 -32687.451656] AUTODETECT spr round 2 (radius: 10) [00:00:47 -28159.714583] AUTODETECT spr round 3 (radius: 15) [00:01:07 -27412.499241] AUTODETECT spr round 4 (radius: 20) [00:01:24 -27192.682649] AUTODETECT spr round 5 (radius: 25) [00:01:35 -27192.659961] SPR radius for FAST iterations: 20 (autodetect) [00:01:35 -27192.659961] Model parameter optimization (eps = 3.000000) [00:01:51 -27125.282845] FAST spr round 1 (radius: 20) [00:02:09 -26381.995965] FAST spr round 2 (radius: 20) [00:02:24 -26368.592585] FAST spr round 3 (radius: 20) [00:02:37 -26362.104831] FAST spr round 4 (radius: 20) [00:02:48 -26360.597824] FAST spr round 5 (radius: 20) [00:02:59 -26360.288434] FAST spr round 6 (radius: 20) [00:03:10 -26360.288395] Model parameter optimization (eps = 1.000000) [00:03:20 -26358.582577] SLOW spr round 1 (radius: 5) [00:03:49 -26351.573044] SLOW spr round 2 (radius: 5) [00:04:13 -26351.572339] SLOW spr round 3 (radius: 10) [00:04:36 -26342.029705] SLOW spr round 4 (radius: 5) [00:05:11 -26341.878189] SLOW spr round 5 (radius: 5) [00:05:40 -26341.878085] SLOW spr round 6 (radius: 10) [00:06:05 -26341.878058] SLOW spr round 7 (radius: 15) [00:06:15] [worker #1] ML tree search #2, logLikelihood: -26335.406832 [00:06:25] [worker #2] ML tree search #3, logLikelihood: -26339.927424 [00:06:43 -26341.878045] SLOW spr round 8 (radius: 20) [00:07:00] [worker #3] ML tree search #4, logLikelihood: -26337.745055 [00:07:18 -26341.878038] SLOW spr round 9 (radius: 25) [00:07:39 -26341.878035] Model parameter optimization (eps = 0.100000) [00:07:42] [worker #0] ML tree search #1, logLikelihood: -26341.869867 [00:07:42 -53427.297978] Initial branch length optimization [00:07:43 -41087.567902] Model parameter optimization (eps = 10.000000) [00:08:02 -40879.886227] AUTODETECT spr round 1 (radius: 5) [00:08:07] [worker #5] ML tree search #6, logLikelihood: -26341.400136 [00:08:13 -33373.410083] AUTODETECT spr round 2 (radius: 10) [00:08:29 -28374.386202] AUTODETECT spr round 3 (radius: 15) [00:08:47 -27264.933160] AUTODETECT spr round 4 (radius: 20) [00:09:05 -27264.911803] SPR radius for FAST iterations: 15 (autodetect) [00:09:05 -27264.911803] Model parameter optimization (eps = 3.000000) [00:09:18 -27195.571103] FAST spr round 1 (radius: 15) [00:09:25] [worker #4] ML tree search #5, logLikelihood: -26337.023800 [00:09:36 -26403.298118] FAST spr round 2 (radius: 15) [00:09:52 -26356.688764] FAST spr round 3 (radius: 15) [00:10:04 -26353.990346] FAST spr round 4 (radius: 15) [00:10:17 -26352.037318] FAST spr round 5 (radius: 15) [00:10:29 -26346.988663] FAST spr round 6 (radius: 15) [00:10:40 -26346.845354] FAST spr round 7 (radius: 15) [00:10:51 -26346.767333] Model parameter optimization (eps = 1.000000) [00:10:59 -26345.385253] SLOW spr round 1 (radius: 5) [00:11:27 -26340.247698] SLOW spr round 2 (radius: 5) [00:11:51 -26339.931248] SLOW spr round 3 (radius: 5) [00:12:14 -26339.931223] SLOW spr round 4 (radius: 10) [00:12:38 -26339.931212] SLOW spr round 5 (radius: 15) [00:13:01] [worker #2] ML tree search #9, logLikelihood: -26340.173447 [00:13:09] [worker #3] ML tree search #10, logLikelihood: -26348.055275 [00:13:16 -26339.931207] SLOW spr round 6 (radius: 20) [00:13:50 -26339.931204] SLOW spr round 7 (radius: 25) [00:14:00] [worker #1] ML tree search #8, logLikelihood: -26337.750202 [00:14:12 -26339.931202] Model parameter optimization (eps = 0.100000) [00:14:16] [worker #0] ML tree search #7, logLikelihood: -26339.696626 [00:14:16 -53839.923845] Initial branch length optimization [00:14:17 -41372.862640] Model parameter optimization (eps = 10.000000) [00:14:33 -41149.909417] AUTODETECT spr round 1 (radius: 5) [00:14:44 -34502.080330] AUTODETECT spr round 2 (radius: 10) [00:15:01 -29313.752904] AUTODETECT spr round 3 (radius: 15) [00:15:10] [worker #5] ML tree search #12, logLikelihood: -26350.016413 [00:15:20 -28005.668342] AUTODETECT spr round 4 (radius: 20) [00:15:38 -27922.164415] AUTODETECT spr round 5 (radius: 25) [00:15:48 -27922.133847] SPR radius for FAST iterations: 20 (autodetect) [00:15:48 -27922.133847] Model parameter optimization (eps = 3.000000) [00:16:04 -27843.818162] FAST spr round 1 (radius: 20) [00:16:21 -26432.382643] FAST spr round 2 (radius: 20) [00:16:36 -26379.677204] FAST spr round 3 (radius: 20) [00:16:49 -26374.468018] FAST spr round 4 (radius: 20) [00:17:01 -26373.252096] FAST spr round 5 (radius: 20) [00:17:13 -26372.597263] FAST spr round 6 (radius: 20) [00:17:25 -26371.564708] FAST spr round 7 (radius: 20) [00:17:37 -26369.590825] FAST spr round 8 (radius: 20) [00:17:48 -26369.449913] FAST spr round 9 (radius: 20) [00:17:59 -26369.330143] FAST spr round 10 (radius: 20) [00:18:10 -26369.067198] FAST spr round 11 (radius: 20) [00:18:22 -26369.067133] Model parameter optimization (eps = 1.000000) [00:18:24] [worker #4] ML tree search #11, logLikelihood: -26339.551207 [00:18:38 -26355.758239] SLOW spr round 1 (radius: 5) [00:19:05 -26351.766116] SLOW spr round 2 (radius: 5) [00:19:15] [worker #2] ML tree search #15, logLikelihood: -26338.908184 [00:19:29 -26351.765604] SLOW spr round 3 (radius: 10) [00:19:53 -26351.178628] SLOW spr round 4 (radius: 5) [00:20:28 -26351.177478] SLOW spr round 5 (radius: 10) [00:20:57 -26351.177384] SLOW spr round 6 (radius: 15) [00:21:17] [worker #1] ML tree search #14, logLikelihood: -26340.140782 [00:21:33 -26351.177363] SLOW spr round 7 (radius: 20) [00:22:08 -26351.177355] SLOW spr round 8 (radius: 25) [00:22:20] [worker #5] ML tree search #18, logLikelihood: -26338.011216 [00:22:30] [worker #3] ML tree search #16, logLikelihood: -26337.388200 [00:22:31 -26351.177350] Model parameter optimization (eps = 0.100000) [00:22:34] [worker #0] ML tree search #13, logLikelihood: -26351.159280 [00:22:35 -53622.420812] Initial branch length optimization [00:22:35 -41224.580677] Model parameter optimization (eps = 10.000000) [00:22:53 -41032.689780] AUTODETECT spr round 1 (radius: 5) [00:23:04 -34833.502538] AUTODETECT spr round 2 (radius: 10) [00:23:20 -30683.164868] AUTODETECT spr round 3 (radius: 15) [00:23:39 -28711.007544] AUTODETECT spr round 4 (radius: 20) [00:23:59 -28312.986218] AUTODETECT spr round 5 (radius: 25) [00:24:12 -28312.964195] SPR radius for FAST iterations: 20 (autodetect) [00:24:12 -28312.964195] Model parameter optimization (eps = 3.000000) [00:24:26] [worker #4] ML tree search #17, logLikelihood: -26337.522694 [00:24:33 -28242.458866] FAST spr round 1 (radius: 20) [00:24:54 -26492.753331] FAST spr round 2 (radius: 20) [00:25:11 -26379.359907] FAST spr round 3 (radius: 20) [00:25:23 -26370.223496] FAST spr round 4 (radius: 20) [00:25:36 -26365.993277] FAST spr round 5 (radius: 20) [00:25:47 -26365.126749] FAST spr round 6 (radius: 20) [00:25:58 -26365.126749] Model parameter optimization (eps = 1.000000) [00:26:16 -26346.541402] SLOW spr round 1 (radius: 5) [00:26:44 -26340.648178] SLOW spr round 2 (radius: 5) [00:27:09 -26340.164393] SLOW spr round 3 (radius: 5) [00:27:32 -26340.164069] SLOW spr round 4 (radius: 10) [00:27:46] [worker #1] ML tree search #20, logLikelihood: -26340.848540 [00:27:55 -26340.164060] SLOW spr round 5 (radius: 15) [00:28:36 -26340.164057] SLOW spr round 6 (radius: 20) [00:29:09 -26340.164056] SLOW spr round 7 (radius: 25) [00:29:31 -26340.164055] Model parameter optimization (eps = 0.100000) [00:29:35] [worker #0] ML tree search #19, logLikelihood: -26340.051036 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.113051,0.434665) (0.063630,0.523857) (0.493216,0.971329) (0.330103,1.328230) 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: -26335.406832 AIC score: 53180.813663 / AICc score: 58857.335402 / BIC score: 54106.772668 Free parameters (model + branch lengths): 255 WARNING: Best ML tree contains 4 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8MTL3/3_mltree/A8MTL3.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8MTL3/3_mltree/A8MTL3.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8MTL3/3_mltree/A8MTL3.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8MTL3/3_mltree/A8MTL3.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8MTL3/3_mltree/A8MTL3.raxml.log Analysis started: 26-Jul-2021 00:10:22 / finished: 26-Jul-2021 00:39:58 Elapsed time: 1775.416 seconds Consumed energy: 94.223 Wh