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 04-Jun-2021 13:35:18 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96MT3/2_msa/Q96MT3_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96MT3/3_mltree/Q96MT3.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96MT3/4_raxmlng_ancestral/Q96MT3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802918 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96MT3/2_msa/Q96MT3_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 831 sites WARNING: Sequences tr_B4QNC5_B4QNC5_DROSI_7240 and tr_B4HK86_B4HK86_DROSE_7238 are exactly identical! WARNING: Sequences sp_Q90YH9_TES_CHICK_9031 and tr_G1N9U9_G1N9U9_MELGA_9103 are exactly identical! WARNING: Sequences tr_M3XMP2_M3XMP2_MUSPF_9669 and tr_A0A2Y9KQB3_A0A2Y9KQB3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I2YBT3_A0A2I2YBT3_GORGO_9595 and tr_A0A2I3RJU1_A0A2I3RJU1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YBT3_A0A2I2YBT3_GORGO_9595 and sp_Q7Z3G6_PRIC2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YBT3_A0A2I2YBT3_GORGO_9595 and tr_A0A2R9BCV0_A0A2R9BCV0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZKB1_A0A2I2ZKB1_GORGO_9595 and sp_Q5RC52_TES_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2ZKB1_A0A2I2ZKB1_GORGO_9595 and sp_Q2QLF4_TES_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZKB1_A0A2I2ZKB1_GORGO_9595 and sp_Q9UGI8_TES_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZKB1_A0A2I2ZKB1_GORGO_9595 and tr_A0A2R9B6X8_A0A2R9B6X8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SDR1_G3SDR1_GORGO_9595 and tr_K7EV16_K7EV16_PONAB_9601 are exactly identical! WARNING: Sequences tr_H2PAC0_H2PAC0_PONAB_9601 and tr_A0A1D5QIH0_A0A1D5QIH0_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PAC0_H2PAC0_PONAB_9601 and tr_G7NZA3_G7NZA3_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2PAC0_H2PAC0_PONAB_9601 and tr_A0A096MXL5_A0A096MXL5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PAC0_H2PAC0_PONAB_9601 and tr_A0A0D9RHR1_A0A0D9RHR1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PAC0_H2PAC0_PONAB_9601 and tr_A0A2K5LJP2_A0A2K5LJP2_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PAC0_H2PAC0_PONAB_9601 and tr_A0A2K5ZH77_A0A2K5ZH77_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1SV99_G1SV99_RABIT_9986 and sp_Q09YN8_TES_RABIT_9986 are exactly identical! WARNING: Sequences sp_A0M8U6_TES_CANLF_9615 and tr_F1PFX9_F1PFX9_CANLF_9615 are exactly identical! WARNING: Sequences sp_A0M8U6_TES_CANLF_9615 and tr_A0A2Y9JY25_A0A2Y9JY25_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3TH70_A0A2I3TH70_PANTR_9598 and tr_A0A2R9CEK7_A0A2R9CEK7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TJ78_A0A2I3TJ78_PANTR_9598 and tr_H2R2U9_H2R2U9_PANTR_9598 are exactly identical! WARNING: Sequences tr_K7DBC5_K7DBC5_PANTR_9598 and tr_A0A2R9C4Z4_A0A2R9C4Z4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6XY88_F6XY88_HORSE_9796 and sp_Q2QLB2_TES_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q09YJ2_TES_SHEEP_9940 and tr_A0A2U3V8W9_A0A2U3V8W9_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q09YJ2_TES_SHEEP_9940 and tr_A0A2Y9NZP9_A0A2Y9NZP9_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q09YJ2_TES_SHEEP_9940 and tr_A0A384B7C7_A0A384B7C7_BALAS_310752 are exactly identical! WARNING: Sequences tr_H0X1V8_H0X1V8_OTOGA_30611 and sp_Q2QLH9_TES_OTOGA_30611 are exactly identical! WARNING: Sequences tr_F6VGC9_F6VGC9_MACMU_9544 and tr_A0A2K5MSR6_A0A2K5MSR6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7ERF2_F7ERF2_MACMU_9544 and tr_G7P2I2_G7P2I2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7ERF2_F7ERF2_MACMU_9544 and tr_A0A096NU86_A0A096NU86_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7ERF2_F7ERF2_MACMU_9544 and sp_A0M8R4_TES_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7ERF2_F7ERF2_MACMU_9544 and tr_A0A0D9REW2_A0A0D9REW2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7ERF2_F7ERF2_MACMU_9544 and tr_A0A2K5KYD6_A0A2K5KYD6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7ERF2_F7ERF2_MACMU_9544 and tr_A0A2K5ZZJ3_A0A2K5ZZJ3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HTI7_F7HTI7_MACMU_9544 and tr_G7PHM3_G7PHM3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MKT4_G7MKT4_MACMU_9544 and tr_G7NYW0_G7NYW0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MKT4_G7MKT4_MACMU_9544 and tr_A0A2I3LU89_A0A2I3LU89_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7MKT4_G7MKT4_MACMU_9544 and tr_A0A2K5L289_A0A2K5L289_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MKT4_G7MKT4_MACMU_9544 and tr_A0A2K5YCV8_A0A2K5YCV8_MANLE_9568 are exactly identical! WARNING: Sequences tr_E5SIJ8_E5SIJ8_TRISP_6334 and tr_A0A0V0WWT7_A0A0V0WWT7_9BILA_92179 are exactly identical! WARNING: Sequences tr_G3TIJ8_G3TIJ8_LOXAF_9785 and sp_Q108U9_TES_LOXAF_9785 are exactly identical! WARNING: Sequences tr_F4WW72_F4WW72_ACREC_103372 and tr_A0A195B297_A0A195B297_9HYME_520822 are exactly identical! WARNING: Sequences tr_G0MM05_G0MM05_CAEBE_135651 and tr_G0P7J2_G0P7J2_CAEBE_135651 are exactly identical! WARNING: Sequences tr_A0A0V0RR11_A0A0V0RR11_9BILA_6336 and tr_A0A0V0TYW3_A0A0V0TYW3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1D7Z7_A0A0V1D7Z7_TRIBR_45882 and tr_A0A0V0UUR5_A0A0V0UUR5_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DB32_A0A0V1DB32_TRIBR_45882 and tr_A0A0V0VQS6_A0A0V0VQS6_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A226MDW1_A0A226MDW1_CALSU_9009 and tr_A0A226PFS6_A0A226PFS6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2A2JNE2_A0A2A2JNE2_9BILA_2018661 and tr_A0A2A2K760_A0A2A2K760_9BILA_2018661 are exactly identical! WARNING: Sequences tr_A0A2D0PIE0_A0A2D0PIE0_ICTPU_7998 and tr_A0A2D0PJU7_A0A2D0PJU7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4CCL9_A0A2U4CCL9_TURTR_9739 and tr_A0A2U4CCM2_A0A2U4CCM2_TURTR_9739 are exactly identical! WARNING: Duplicate sequences found: 51 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96MT3/4_raxmlng_ancestral/Q96MT3.raxml.reduced.phy Alignment comprises 1 partitions and 831 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 831 Gaps: 49.79 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96MT3/4_raxmlng_ancestral/Q96MT3.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96MT3/3_mltree/Q96MT3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 208 / 16640 [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: -221007.658829 [00:00:00 -221007.658829] Initial branch length optimization [00:00:02 -204785.404262] Model parameter optimization (eps = 0.100000) [00:01:04] Tree #1, final logLikelihood: -204247.006184 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.089666,0.201152) (0.057542,0.280824) (0.299821,0.632170) (0.552971,1.403810) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96MT3/4_raxmlng_ancestral/Q96MT3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96MT3/4_raxmlng_ancestral/Q96MT3.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96MT3/4_raxmlng_ancestral/Q96MT3.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96MT3/4_raxmlng_ancestral/Q96MT3.raxml.log Analysis started: 04-Jun-2021 13:35:18 / finished: 04-Jun-2021 13:36:30 Elapsed time: 72.011 seconds