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 12-Jul-2021 17:59:06 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NSI8/2_msa/Q9NSI8_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NSI8/3_mltree/Q9NSI8.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NSI8/4_raxmlng_ancestral/Q9NSI8 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101946 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/300621_run/phylogeny-snakemake/results/Q9NSI8/2_msa/Q9NSI8_nogap_msa.fasta [00:00:00] Loaded alignment with 657 taxa and 373 sites WARNING: Sequences tr_B4QZX9_B4QZX9_DROSI_7240 and tr_A0A0B4KHV7_A0A0B4KHV7_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QZX9_B4QZX9_DROSI_7240 and tr_B4HE50_B4HE50_DROSE_7238 are exactly identical! WARNING: Sequences sp_P27870_VAV_MOUSE_10090 and sp_P54100_VAV_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Z155_M3Z155_MUSPF_9669 and tr_A0A2Y9KK10_A0A2Y9KK10_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z2Z1_M3Z2Z1_MUSPF_9669 and tr_A0A2Y9JFD5_A0A2Y9JFD5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3R3J1_G3R3J1_GORGO_9595 and sp_O94885_SASH1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RGS3_G3RGS3_GORGO_9595 and tr_H2R020_H2R020_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RGS3_G3RGS3_GORGO_9595 and tr_A0A2R9BE84_A0A2R9BE84_PANPA_9597 are exactly identical! WARNING: Sequences tr_C3XY49_C3XY49_BRAFL_7739 and tr_C3XY50_C3XY50_BRAFL_7739 are exactly identical! WARNING: Sequences tr_H2QF58_H2QF58_PANTR_9598 and sp_P15498_VAV_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A1D5Q9M6_A0A1D5Q9M6_MACMU_9544 and tr_G7P4Z9_G7P4Z9_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5Q9M6_A0A1D5Q9M6_MACMU_9544 and tr_A0A2K6DQI4_A0A2K6DQI4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5R6I9_A0A1D5R6I9_MACMU_9544 and tr_G7Q3N3_G7Q3N3_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5R6I9_A0A1D5R6I9_MACMU_9544 and tr_A0A0D9R7C4_A0A0D9R7C4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5R6I9_A0A1D5R6I9_MACMU_9544 and tr_A0A2K5M0W2_A0A2K5M0W2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5R6I9_A0A1D5R6I9_MACMU_9544 and tr_A0A2K6B2K9_A0A2K6B2K9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5R6I9_A0A1D5R6I9_MACMU_9544 and tr_A0A2K6A115_A0A2K6A115_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7BD31_F7BD31_MACMU_9544 and tr_A0A2I3MBF6_A0A2I3MBF6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7BD31_F7BD31_MACMU_9544 and tr_A0A2K5KNR1_A0A2K5KNR1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7BD31_F7BD31_MACMU_9544 and tr_A0A2K6BD32_A0A2K6BD32_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BD31_F7BD31_MACMU_9544 and tr_A0A2K5Y133_A0A2K5Y133_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GVH2_F7GVH2_MACMU_9544 and tr_A0A2K6BCP1_A0A2K6BCP1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NMM1_G7NMM1_MACMU_9544 and tr_G7PYV3_G7PYV3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7NMM1_G7NMM1_MACMU_9544 and tr_A0A0A0MUN9_A0A0A0MUN9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NMM1_G7NMM1_MACMU_9544 and tr_A0A2K5Y550_A0A2K5Y550_MANLE_9568 are exactly identical! WARNING: Sequences tr_G2YJP8_G2YJP8_BOTF4_999810 and tr_M7V328_M7V328_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_L0PC91_L0PC91_PNEJ8_1209962 and tr_A0A0W4ZP01_A0A0W4ZP01_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_V2X632_V2X632_MONRO_1381753 and tr_A0A0W0F3E3_A0A0W0F3E3_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015JCM5_A0A015JCM5_9GLOM_1432141 and tr_A0A2H5TPG1_A0A2H5TPG1_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A158N8G8_A0A158N8G8_ONCVO_6282 and tr_A0A182DWY6_A0A182DWY6_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A094EI17_A0A094EI17_9PEZI_1420912 and tr_A0A1B8GW90_A0A1B8GW90_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A151MDT3_A0A151MDT3_ALLMI_8496 and tr_A0A1U8D476_A0A1U8D476_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A194QR65_A0A194QR65_PAPMA_76193 and tr_A0A0N1PGN2_A0A0N1PGN2_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A2I0MU66_A0A2I0MU66_COLLI_8932 and tr_A0A1V4JLG1_A0A1V4JLG1_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0RX04_A0A0V0RX04_9BILA_6336 and tr_A0A0V1D4X7_A0A0V1D4X7_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RX04_A0A0V0RX04_9BILA_6336 and tr_A0A0V0WL95_A0A0V0WL95_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RX04_A0A0V0RX04_9BILA_6336 and tr_A0A0V1LEA7_A0A0V1LEA7_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0RX04_A0A0V0RX04_9BILA_6336 and tr_A0A0V1P550_A0A0V1P550_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RX04_A0A0V0RX04_9BILA_6336 and tr_A0A0V0UIJ3_A0A0V0UIJ3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A226NIB8_A0A226NIB8_CALSU_9009 and tr_A0A226PUH2_A0A226PUH2_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226M8I4_A0A226M8I4_COLVI_9014 and tr_A0A226M9K3_A0A226M9K3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0T374_A0A2D0T374_ICTPU_7998 and tr_A0A2D0T382_A0A2D0T382_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T374_A0A2D0T374_ICTPU_7998 and tr_A0A2D0T390_A0A2D0T390_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T374_A0A2D0T374_ICTPU_7998 and tr_A0A2D0T3A9_A0A2D0T3A9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T374_A0A2D0T374_ICTPU_7998 and tr_A0A2D0T431_A0A2D0T431_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T374_A0A2D0T374_ICTPU_7998 and tr_W5UK77_W5UK77_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2Y9F5Y0_A0A2Y9F5Y0_PHYCD_9755 and tr_A0A383Z243_A0A383Z243_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 47 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NSI8/4_raxmlng_ancestral/Q9NSI8.raxml.reduced.phy Alignment comprises 1 partitions and 373 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 373 Gaps: 31.94 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NSI8/4_raxmlng_ancestral/Q9NSI8.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/300621_run/phylogeny-snakemake/results/Q9NSI8/3_mltree/Q9NSI8.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 94 / 7520 [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: -180785.257688 [00:00:00 -180785.257688] Initial branch length optimization [00:00:01 -113416.056853] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -112724.832285 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.187256,0.621748) (0.090605,0.542677) (0.385153,0.699457) (0.336987,1.676646) 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/300621_run/phylogeny-snakemake/results/Q9NSI8/4_raxmlng_ancestral/Q9NSI8.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NSI8/4_raxmlng_ancestral/Q9NSI8.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NSI8/4_raxmlng_ancestral/Q9NSI8.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NSI8/4_raxmlng_ancestral/Q9NSI8.raxml.log Analysis started: 12-Jul-2021 17:59:06 / finished: 12-Jul-2021 17:59:51 Elapsed time: 44.292 seconds Consumed energy: 3.942 Wh