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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 18:31:15 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43909/2_msa/O43909_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43909/3_mltree/O43909.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43909/4_raxmlng_ancestral/O43909 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647875 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43909/2_msa/O43909_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 919 sites WARNING: Sequences sp_P97464_EXT1_MOUSE_10090 and tr_G3V901_G3V901_RAT_10116 are exactly identical! WARNING: Sequences tr_H2PR27_H2PR27_PONAB_9601 and tr_K7DAN3_K7DAN3_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PR27_H2PR27_PONAB_9601 and tr_F7F8Y3_F7F8Y3_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PR27_H2PR27_PONAB_9601 and sp_A9X1C8_EXT1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PR27_H2PR27_PONAB_9601 and tr_A0A2K5P351_A0A2K5P351_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PR27_H2PR27_PONAB_9601 and tr_A0A2K6E3M4_A0A2K6E3M4_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PR27_H2PR27_PONAB_9601 and tr_A0A2R8ZLS5_A0A2R8ZLS5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3S6F0_A0A2I3S6F0_PANTR_9598 and tr_A0A2R9BBR6_A0A2R9BBR6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SQC4_A0A2I3SQC4_PANTR_9598 and tr_A0A2R9C8L9_A0A2R9C8L9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NHG3_A0A158NHG3_ATTCE_12957 and tr_A0A195BXS6_A0A195BXS6_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0E0HHI6_A0A0E0HHI6_ORYNI_4536 and tr_A0A0E0PQJ6_A0A0E0PQJ6_ORYRU_4529 are exactly identical! WARNING: Sequences tr_F6S245_F6S245_MACMU_9544 and tr_A0A2K6DSA0_A0A2K6DSA0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7N0T1_G7N0T1_MACMU_9544 and tr_G7PD46_G7PD46_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7N0T1_G7N0T1_MACMU_9544 and tr_A0A2K6D518_A0A2K6D518_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7N0T1_G7N0T1_MACMU_9544 and tr_A0A2K5ZV76_A0A2K5ZV76_MANLE_9568 are exactly identical! WARNING: Sequences sp_A2Y6Z7_GINT1_ORYSI_39946 and sp_Q53WK1_GINT1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G7PQC9_G7PQC9_MACFA_9541 and tr_A0A2K5KHT3_A0A2K5KHT3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PQC9_G7PQC9_MACFA_9541 and tr_A0A2K6AXZ7_A0A2K6AXZ7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0JN91_A0JN91_BOVIN_9913 and sp_O77783_EXT2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_N4UZ74_N4UZ74_FUSC1_1229664 and tr_A0A2H3TKZ2_A0A2H3TKZ2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_N4UZ74_N4UZ74_FUSC1_1229664 and tr_A0A2H3GXA5_A0A2H3GXA5_FUSOX_327505 are exactly identical! WARNING: Sequences tr_A0A067FSA3_A0A067FSA3_CITSI_2711 and tr_V4SMC2_V4SMC2_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067FSA3_A0A067FSA3_CITSI_2711 and tr_A0A2H5NJZ6_A0A2H5NJZ6_CITUN_55188 are exactly identical! WARNING: Sequences tr_V4UBE2_V4UBE2_9ROSI_85681 and tr_A0A2H5NWN0_A0A2H5NWN0_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A091FWW6_A0A091FWW6_CORBR_85066 and tr_A0A093Q8T2_A0A093Q8T2_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091VMZ4_A0A091VMZ4_NIPNI_128390 and tr_A0A087QY09_A0A087QY09_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VMZ4_A0A091VMZ4_NIPNI_128390 and tr_A0A093I4D1_A0A093I4D1_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091VMZ4_A0A091VMZ4_NIPNI_128390 and tr_A0A093G3S3_A0A093G3S3_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091VMZ4_A0A091VMZ4_NIPNI_128390 and tr_A0A091HPY7_A0A091HPY7_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V1D674_A0A0V1D674_TRIBR_45882 and tr_A0A0V0VBL2_A0A0V0VBL2_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A1S4C0Z2_A0A1S4C0Z2_TOBAC_4097 and tr_A0A1U7VAK4_A0A1U7VAK4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A226MZC2_A0A226MZC2_CALSU_9009 and tr_A0A226PFX6_A0A226PFX6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PT25_A0A2D0PT25_ICTPU_7998 and tr_A0A2D0PVL3_A0A2D0PVL3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V029_A0A2U3V029_TURTR_9739 and tr_A0A2Y9P9E7_A0A2Y9P9E7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3X598_A0A2U3X598_ODORO_9708 and tr_A0A2U3Y7L0_A0A2U3Y7L0_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 35 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43909/4_raxmlng_ancestral/O43909.raxml.reduced.phy Alignment comprises 1 partitions and 919 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 919 Gaps: 42.76 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43909/4_raxmlng_ancestral/O43909.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43909/3_mltree/O43909.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 230 / 18400 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -291276.688699 [00:00:00 -291276.688699] Initial branch length optimization [00:00:02 -269736.737712] Model parameter optimization (eps = 0.100000) [00:01:14] Tree #1, final logLikelihood: -268704.900086 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.127092,0.363415) (0.124526,0.548514) (0.379692,0.760285) (0.368691,1.618796) 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 Marginal ancestral probabilities saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43909/4_raxmlng_ancestral/O43909.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43909/4_raxmlng_ancestral/O43909.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43909/4_raxmlng_ancestral/O43909.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43909/4_raxmlng_ancestral/O43909.raxml.log Analysis started: 02-Jun-2021 18:31:15 / finished: 02-Jun-2021 18:32:38 Elapsed time: 82.973 seconds Consumed energy: 5.124 Wh