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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 02-Jun-2021 18:09:57 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86XK2/2_msa/Q86XK2_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86XK2/3_mltree/Q86XK2.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86XK2/4_raxmlng_ancestral/Q86XK2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622646597 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/Q86XK2/2_msa/Q86XK2_nogap_msa.fasta [00:00:00] Loaded alignment with 657 taxa and 927 sites WARNING: Sequences tr_B4QVX6_B4QVX6_DROSI_7240 and tr_Q9VH60_Q9VH60_DROME_7227 are exactly identical! WARNING: Sequences tr_B4R044_B4R044_DROSI_7240 and tr_B4HZA2_B4HZA2_DROSE_7238 are exactly identical! WARNING: Sequences tr_M3YHV4_M3YHV4_MUSPF_9669 and tr_A0A1S3F9R3_A0A1S3F9R3_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3YHV4_M3YHV4_MUSPF_9669 and tr_A0A2U3V8X0_A0A2U3V8X0_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3YHV4_M3YHV4_MUSPF_9669 and tr_A0A2U3XZR9_A0A2U3XZR9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YHV4_M3YHV4_MUSPF_9669 and tr_A0A2Y9D8L7_A0A2Y9D8L7_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3YHV4_M3YHV4_MUSPF_9669 and tr_A0A2Y9JKT6_A0A2Y9JKT6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1RBE7_G1RBE7_NOMLE_61853 and tr_H2P698_H2P698_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3H5Q6_G3H5Q6_CRIGR_10029 and sp_Q7TSL3_FBX11_RAT_10116 are exactly identical! WARNING: Sequences tr_G3H5Q6_G3H5Q6_CRIGR_10029 and tr_A0A1U7US75_A0A1U7US75_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3R7I8_G3R7I8_GORGO_9595 and tr_H2QHW1_H2QHW1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R7I8_G3R7I8_GORGO_9595 and tr_A0A096NF35_A0A096NF35_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3R7I8_G3R7I8_GORGO_9595 and tr_A0A0D9RMB9_A0A0D9RMB9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1N0L3_G1N0L3_MELGA_9103 and tr_R0K962_R0K962_ANAPL_8839 are exactly identical! WARNING: Sequences tr_Q299I8_Q299I8_DROPS_46245 and tr_B4G581_B4G581_DROPE_7234 are exactly identical! WARNING: Sequences tr_F7CK93_F7CK93_MONDO_13616 and tr_G3W0E3_G3W0E3_SARHA_9305 are exactly identical! WARNING: Sequences tr_M4A965_M4A965_XIPMA_8083 and tr_A0A087YBN3_A0A087YBN3_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A087ZZQ0_A0A087ZZQ0_APIME_7460 and tr_A0A2A3EQB8_A0A2A3EQB8_APICC_94128 are exactly identical! WARNING: Sequences sp_Q86XK2_FBX11_HUMAN_9606 and tr_F7IM67_F7IM67_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q86XK2_FBX11_HUMAN_9606 and tr_A0A2K6BG70_A0A2K6BG70_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FBE7_F7FBE7_MACMU_9544 and tr_G7PW86_G7PW86_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FBE7_F7FBE7_MACMU_9544 and tr_A0A096MQR5_A0A096MQR5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F4WIT3_F4WIT3_ACREC_103372 and tr_A0A151WLY0_A0A151WLY0_9HYME_64791 are exactly identical! WARNING: Sequences tr_F4WIT3_F4WIT3_ACREC_103372 and tr_A0A195FPD9_A0A195FPD9_9HYME_34720 are exactly identical! WARNING: Sequences tr_F4WIT3_F4WIT3_ACREC_103372 and tr_A0A195CTX1_A0A195CTX1_9HYME_456900 are exactly identical! WARNING: Sequences tr_U3K999_U3K999_FICAL_59894 and tr_A0A1U7RI42_A0A1U7RI42_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091IT33_A0A091IT33_EGRGA_188379 and tr_A0A091VMS8_A0A091VMS8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IT33_A0A091IT33_EGRGA_188379 and tr_A0A091WDP5_A0A091WDP5_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091IT33_A0A091IT33_EGRGA_188379 and tr_A0A093G5I2_A0A093G5I2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A0V1CRU3_A0A0V1CRU3_TRIBR_45882 and tr_A0A0V1KUS6_A0A0V1KUS6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CRU3_A0A0V1CRU3_TRIBR_45882 and tr_A0A0V1M6F3_A0A0V1M6F3_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V1CRU3_A0A0V1CRU3_TRIBR_45882 and tr_A0A0V1HU45_A0A0V1HU45_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0V0ZE81_A0A0V0ZE81_9BILA_990121 and tr_A0A0V0TAT1_A0A0V0TAT1_9BILA_144512 are exactly identical! WARNING: Duplicate sequences found: 33 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/Q86XK2/4_raxmlng_ancestral/Q86XK2.raxml.reduced.phy Alignment comprises 1 partitions and 927 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 927 Gaps: 41.55 % Invariant sites: 0.86 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86XK2/4_raxmlng_ancestral/Q86XK2.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/Q86XK2/3_mltree/Q86XK2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 232 / 18560 [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: -182292.683734 [00:00:00 -182292.683734] Initial branch length optimization [00:00:01 -170229.575386] Model parameter optimization (eps = 0.100000) [00:00:49] Tree #1, final logLikelihood: -169152.565697 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.200475,0.606712) (0.129325,0.770698) (0.453425,0.706580) (0.216775,2.114253) 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/Q86XK2/4_raxmlng_ancestral/Q86XK2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86XK2/4_raxmlng_ancestral/Q86XK2.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86XK2/4_raxmlng_ancestral/Q86XK2.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86XK2/4_raxmlng_ancestral/Q86XK2.raxml.log Analysis started: 02-Jun-2021 18:09:57 / finished: 02-Jun-2021 18:10:52 Elapsed time: 54.800 seconds Consumed energy: 3.557 Wh