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 02:03:37 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60832/2_msa/O60832_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60832/3_mltree/O60832.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60832/4_raxmlng_ancestral/O60832 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622675017 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/O60832/2_msa/O60832_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 514 sites WARNING: Sequences tr_J3K814_J3K814_COCIM_246410 and tr_A0A0J6Y8X4_A0A0J6Y8X4_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QGT9_B6QGT9_TALMQ_441960 and tr_A0A093UTR0_A0A093UTR0_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2VU35_B2VU35_PYRTR_426418 and tr_A0A2W1HQM5_A0A2W1HQM5_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3RNN2_G3RNN2_GORGO_9595 and tr_K7CJN9_K7CJN9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RNN2_G3RNN2_GORGO_9595 and sp_O60832_DKC1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q1K6T3_Q1K6T3_NEUCR_367110 and tr_G4UFW9_G4UFW9_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8NSF7_B8NSF7_ASPFN_332952 and tr_Q2UTK8_Q2UTK8_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NSF7_B8NSF7_ASPFN_332952 and tr_A0A1S9D4H7_A0A1S9D4H7_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_F9FZJ5_F9FZJ5_FUSOF_660025 and tr_A0A0D2XCI0_A0A0D2XCI0_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FZJ5_F9FZJ5_FUSOF_660025 and tr_X0DA35_X0DA35_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FZJ5_F9FZJ5_FUSOF_660025 and tr_A0A2H3TGJ6_A0A2H3TGJ6_FUSOX_5507 are exactly identical! WARNING: Sequences tr_E9FAX7_E9FAX7_METRA_655844 and tr_A0A0D9NM69_A0A0D9NM69_METAN_1291518 are exactly identical! WARNING: Sequences tr_J4WFB7_J4WFB7_BEAB2_655819 and tr_A0A0A2VDF9_A0A0A2VDF9_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J4WFB7_J4WFB7_BEAB2_655819 and tr_A0A2N6NNA6_A0A2N6NNA6_BEABA_176275 are exactly identical! WARNING: Sequences tr_G7XS77_G7XS77_ASPKW_1033177 and tr_A0A100IQ80_A0A100IQ80_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XS77_G7XS77_ASPKW_1033177 and tr_A0A146FYU9_A0A146FYU9_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A2YP23_A2YP23_ORYSI_39946 and tr_Q8H5T5_Q8H5T5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F4NZG3_F4NZG3_BATDJ_684364 and tr_A0A177WG50_A0A177WG50_BATDE_403673 are exactly identical! WARNING: Sequences tr_A0A0E0NVL0_A0A0E0NVL0_ORYRU_4529 and tr_Q10KT9_Q10KT9_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F9XHL6_F9XHL6_ZYMTI_336722 and tr_A0A0F4GR06_A0A0F4GR06_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_F9XHL6_F9XHL6_ZYMTI_336722 and tr_A0A1X7S1C7_A0A1X7S1C7_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2Y5Q6_G2Y5Q6_BOTF4_999810 and tr_M7USZ1_M7USZ1_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SND0_F2SND0_TRIRC_559305 and tr_A0A178F3E1_A0A178F3E1_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G3Y4T2_G3Y4T2_ASPNA_380704 and tr_A0A319AU23_A0A319AU23_9EURO_1450533 are exactly identical! WARNING: Sequences tr_S0DTD4_S0DTD4_GIBF5_1279085 and tr_A0A365MQM2_A0A365MQM2_GIBIN_948311 are exactly identical! WARNING: Sequences tr_M2TEI5_M2TEI5_COCSN_665912 and tr_M2T2T9_M2T2T9_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2TEI5_M2TEI5_COCSN_665912 and tr_W6Y7R6_W6Y7R6_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2TEI5_M2TEI5_COCSN_665912 and tr_W6Z9F6_W6Z9F6_COCMI_930090 are exactly identical! WARNING: Sequences tr_V2XJX5_V2XJX5_MONRO_1381753 and tr_A0A0W0EUM1_A0A0W0EUM1_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015LBR3_A0A015LBR3_9GLOM_1432141 and tr_A0A2H5RPL0_A0A2H5RPL0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A9CB73_A9CB73_PAPAN_9555 and tr_A0A0D9R303_A0A0D9R303_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A9CB73_A9CB73_PAPAN_9555 and tr_A0A2K6CD20_A0A2K6CD20_MACNE_9545 are exactly identical! WARNING: Sequences tr_A9CB73_A9CB73_PAPAN_9555 and tr_A0A2K5YY44_A0A2K5YY44_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A094EIB8_A0A094EIB8_9PEZI_1420912 and tr_A0A1B8GST0_A0A1B8GST0_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094EIB8_A0A094EIB8_9PEZI_1420912 and tr_A0A1B8CN80_A0A1B8CN80_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A094EIB8_A0A094EIB8_9PEZI_1420912 and tr_A0A1B8F5F6_A0A1B8F5F6_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_V4RK34_V4RK34_9ROSI_85681 and tr_A0A2H5PQV1_A0A2H5PQV1_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0F0I4Q3_A0A0F0I4Q3_ASPPU_1403190 and tr_A0A2G7FXU4_A0A2G7FXU4_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0V1CVU2_A0A0V1CVU2_TRIBR_45882 and tr_A0A0V1A7J6_A0A0V1A7J6_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CVU2_A0A0V1CVU2_TRIBR_45882 and tr_A0A0V1PEM9_A0A0V1PEM9_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0X164_A0A0V0X164_9BILA_92179 and tr_A0A0V0VXW3_A0A0V0VXW3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0X164_A0A0V0X164_9BILA_92179 and tr_A0A0V1LAW9_A0A0V1LAW9_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0X164_A0A0V0X164_9BILA_92179 and tr_A0A0V0U886_A0A0V0U886_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A117NPT8_A0A117NPT8_9EURO_48697 and tr_A0A1V6NTQ5_A0A1V6NTQ5_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A117NPT8_A0A117NPT8_9EURO_48697 and tr_A0A1V6R2Q7_A0A1V6R2Q7_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A1S3XIQ5_A0A1S3XIQ5_TOBAC_4097 and tr_A0A1U7XNN1_A0A1U7XNN1_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2S7P993_A0A2S7P993_9HELO_2070414 and tr_A0A2S7Q4Y7_A0A2S7Q4Y7_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A2U4BIG9_A0A2U4BIG9_TURTR_9739 and tr_A0A2Y9MLZ2_A0A2Y9MLZ2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2V5HXI2_A0A2V5HXI2_9EURO_1450541 and tr_A0A2V5IDS9_A0A2V5IDS9_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 49 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/O60832/4_raxmlng_ancestral/O60832.raxml.reduced.phy Alignment comprises 1 partitions and 514 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 514 Gaps: 12.65 % Invariant sites: 2.14 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60832/4_raxmlng_ancestral/O60832.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/O60832/3_mltree/O60832.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 129 / 10320 [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: -161750.170242 [00:00:00 -161750.170242] Initial branch length optimization [00:00:01 -153228.047137] Model parameter optimization (eps = 0.100000) [00:00:44] Tree #1, final logLikelihood: -152554.791973 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.267746,0.188774) (0.297330,0.294280) (0.181018,0.911494) (0.253907,2.744954) 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/O60832/4_raxmlng_ancestral/O60832.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60832/4_raxmlng_ancestral/O60832.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60832/4_raxmlng_ancestral/O60832.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60832/4_raxmlng_ancestral/O60832.raxml.log Analysis started: 03-Jun-2021 02:03:37 / finished: 03-Jun-2021 02:04:26 Elapsed time: 49.025 seconds Consumed energy: 4.348 Wh