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 03-Jun-2021 02:25:30 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01726/2_msa/Q01726_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01726/3_mltree/Q01726.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01726/4_raxmlng_ancestral/Q01726 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676330 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/Q01726/2_msa/Q01726_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 317 sites WARNING: Sequences tr_A0A1D5P8Y9_A0A1D5P8Y9_CHICK_9031 and tr_A0A226NGX6_A0A226NGX6_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5P8Y9_A0A1D5P8Y9_CHICK_9031 and tr_A0A226P9F8_A0A226P9F8_COLVI_9014 are exactly identical! WARNING: Sequences tr_M3Z6F0_M3Z6F0_MUSPF_9669 and tr_A0A2U3WYM4_A0A2U3WYM4_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3H7W5_A0A2I3H7W5_NOMLE_61853 and tr_U3C187_U3C187_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1SA07_G1SA07_NOMLE_61853 and tr_G3RGA2_G3RGA2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1SA07_G1SA07_NOMLE_61853 and sp_P32245_MC4R_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1SA07_G1SA07_NOMLE_61853 and tr_C3U0E1_C3U0E1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QEX9_G3QEX9_GORGO_9595 and tr_A0A2J8L555_A0A2J8L555_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QEX9_G3QEX9_GORGO_9595 and sp_P47775_GPR12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QEX9_G3QEX9_GORGO_9595 and tr_A0A2R8ZDQ5_A0A2R8ZDQ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QPS8_G3QPS8_GORGO_9595 and sp_Q01718_ACTHR_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RVT2_G3RVT2_GORGO_9595 and sp_Q864K9_MSHR_GORGO_9595 are exactly identical! WARNING: Sequences tr_G3S902_G3S902_GORGO_9595 and tr_H2RHZ6_H2RHZ6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S902_G3S902_GORGO_9595 and sp_P18089_ADA2B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S902_G3S902_GORGO_9595 and tr_A0A2R8ZLT2_A0A2R8ZLT2_PANPA_9597 are exactly identical! WARNING: Sequences tr_F1Q1Q4_F1Q1Q4_CANLF_9615 and tr_M3X1F7_M3X1F7_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1Q1Q4_F1Q1Q4_CANLF_9615 and tr_A0A2U3VWU6_A0A2U3VWU6_ODORO_9708 are exactly identical! WARNING: Sequences tr_F7G5U3_F7G5U3_MONDO_13616 and tr_G3VWZ4_G3VWZ4_SARHA_9305 are exactly identical! WARNING: Sequences tr_I3N755_I3N755_ICTTR_43179 and tr_A0A384C7M7_A0A384C7M7_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A1D5Q666_A0A1D5Q666_MACMU_9544 and tr_G7PVW4_G7PVW4_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5Q666_A0A1D5Q666_MACMU_9544 and tr_A0A096MKY0_A0A096MKY0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q666_A0A1D5Q666_MACMU_9544 and tr_A0A2K6AT84_A0A2K6AT84_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5Q666_A0A1D5Q666_MACMU_9544 and tr_A0A2K5XBL9_A0A2K5XBL9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1D5R418_A0A1D5R418_MACMU_9544 and tr_G8F545_G8F545_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6TP71_F6TP71_MACMU_9544 and tr_A0A0D9SDD1_A0A0D9SDD1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GYJ1_F7GYJ1_MACMU_9544 and tr_G7PWW2_G7PWW2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GYJ1_F7GYJ1_MACMU_9544 and tr_A0A0D9SB59_A0A0D9SB59_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GYJ1_F7GYJ1_MACMU_9544 and tr_A0A2K5L3Q4_A0A2K5L3Q4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GYJ1_F7GYJ1_MACMU_9544 and tr_A0A2K6B127_A0A2K6B127_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GYJ1_F7GYJ1_MACMU_9544 and tr_A0A2K5XRZ6_A0A2K5XRZ6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7NAM7_G7NAM7_MACMU_9544 and tr_A0A0D9SDJ5_A0A0D9SDJ5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7NAM7_G7NAM7_MACMU_9544 and tr_A0A2K5KPM6_A0A2K5KPM6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NAM7_G7NAM7_MACMU_9544 and tr_A0A2K6AYU9_A0A2K6AYU9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NAM7_G7NAM7_MACMU_9544 and tr_A0A2K5XWB1_A0A2K5XWB1_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YUR0_H0YUR0_TAEGU_59729 and tr_A0A218V0D3_A0A218V0D3_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZMU0_H0ZMU0_TAEGU_59729 and tr_A0A091UQC0_A0A091UQC0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A287B7L8_A0A287B7L8_PIG_9823 and tr_F1RSY6_F1RSY6_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A151NYX0_A0A151NYX0_ALLMI_8496 and tr_A0A1U7RHN4_A0A1U7RHN4_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091JK67_A0A091JK67_EGRGA_188379 and tr_A0A091V1V2_A0A091V1V2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JPY7_A0A091JPY7_EGRGA_188379 and tr_A0A0A0APS7_A0A0A0APS7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087R202_A0A087R202_APTFO_9233 and tr_A0A0A0AEP4_A0A0A0AEP4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087RBC4_A0A087RBC4_APTFO_9233 and tr_A0A0A0ASN7_A0A0A0ASN7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0MCM8_A0A2I0MCM8_COLLI_8932 and tr_A0A1V4K9L6_A0A1V4K9L6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MW64_A0A2I0MW64_COLLI_8932 and tr_A0A1V4JWJ0_A0A1V4JWJ0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A195EDS6_A0A195EDS6_9HYME_471704 and tr_A0A195FHQ1_A0A195FHQ1_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1U7Q2G7_A0A1U7Q2G7_MESAU_10036 and sp_P70115_ACTHR_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A226NH60_A0A226NH60_CALSU_9009 and tr_A0A226PAI2_A0A226PAI2_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NLR8_A0A226NLR8_CALSU_9009 and tr_A0A226PYT8_A0A226PYT8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4AUW8_A0A2U4AUW8_TURTR_9739 and tr_A0A2Y9MB95_A0A2Y9MB95_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3ZM36_A0A2U3ZM36_ODORO_9708 and tr_A0A2U3XDH5_A0A2U3XDH5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9QBD7_A0A2Y9QBD7_DELLE_9749 and tr_A0A2Y9FAH5_A0A2Y9FAH5_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 51 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/Q01726/4_raxmlng_ancestral/Q01726.raxml.reduced.phy Alignment comprises 1 partitions and 317 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 317 Gaps: 14.34 % Invariant sites: 0.32 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01726/4_raxmlng_ancestral/Q01726.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/Q01726/3_mltree/Q01726.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 80 / 6400 [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: -112233.890663 [00:00:00 -112233.890663] Initial branch length optimization [00:00:00 -111558.719615] Model parameter optimization (eps = 0.100000) [00:00:20] Tree #1, final logLikelihood: -111156.505150 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.194147,0.389487) (0.246851,0.407569) (0.377790,0.975492) (0.181212,2.512209) 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/Q01726/4_raxmlng_ancestral/Q01726.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01726/4_raxmlng_ancestral/Q01726.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01726/4_raxmlng_ancestral/Q01726.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01726/4_raxmlng_ancestral/Q01726.raxml.log Analysis started: 03-Jun-2021 02:25:30 / finished: 03-Jun-2021 02:25:54 Elapsed time: 23.539 seconds Consumed energy: 1.384 Wh