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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 23-Jun-2021 00:27:41 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O15160/2_msa/O15160_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O15160/3_mltree/O15160.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O15160/4_raxmlng_ancestral/O15160 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624397261 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/030621_run/phylogeny-snakemake/results/O15160/2_msa/O15160_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 346 sites WARNING: Sequences tr_A0A0E1S3F3_A0A0E1S3F3_COCIM_246410 and tr_A0A0J6YCM9_A0A0J6YCM9_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6Q738_B6Q738_TALMQ_441960 and tr_A0A093VGX7_A0A093VGX7_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WCA1_B2WCA1_PYRTR_426418 and tr_A0A2W1CUT2_A0A2W1CUT2_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A2I2YY45_A0A2I2YY45_GORGO_9595 and tr_A0A2I3SZS6_A0A2I3SZS6_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YY45_A0A2I2YY45_GORGO_9595 and sp_O15160_RPAC1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YY45_A0A2I2YY45_GORGO_9595 and tr_A0A2R9CJQ8_A0A2R9CJQ8_PANPA_9597 are exactly identical! WARNING: Sequences tr_B8NHK8_B8NHK8_ASPFN_332952 and tr_Q2UFF5_Q2UFF5_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NHK8_B8NHK8_ASPFN_332952 and tr_A0A1S9E105_A0A1S9E105_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NHK8_B8NHK8_ASPFN_332952 and tr_A0A2G7FLV3_A0A2G7FLV3_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179UM16_A0A179UM16_BLAGS_559298 and tr_C5GBG6_C5GBG6_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9G337_F9G337_FUSOF_660025 and tr_A0A0D2X9X7_A0A0D2X9X7_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9G337_F9G337_FUSOF_660025 and tr_X0BXK6_X0BXK6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9G337_F9G337_FUSOF_660025 and tr_A0A2H3SW42_A0A2H3SW42_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9G337_F9G337_FUSOF_660025 and tr_A0A2H3HVK4_A0A2H3HVK4_FUSOX_327505 are exactly identical! WARNING: Sequences tr_C6HA00_C6HA00_AJECH_544712 and tr_F0UKW3_F0UKW3_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0E0GL64_A0A0E0GL64_ORYNI_4536 and tr_A0A0E0NTS0_A0A0E0NTS0_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GL64_A0A0E0GL64_ORYNI_4536 and tr_A0A0D3FHA5_A0A0D3FHA5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GL64_A0A0E0GL64_ORYNI_4536 and tr_A0A0D9Z5W8_A0A0D9Z5W8_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0GL64_A0A0E0GL64_ORYNI_4536 and tr_Q10MU2_Q10MU2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G7MPF0_G7MPF0_MACMU_9544 and tr_G8F4F6_G8F4F6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MPF0_G7MPF0_MACMU_9544 and tr_A0A2K6B6N1_A0A2K6B6N1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7X521_G7X521_ASPKW_1033177 and tr_A0A100I4H3_A0A100I4H3_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7X521_G7X521_ASPKW_1033177 and tr_A0A146FM37_A0A146FM37_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7X521_G7X521_ASPKW_1033177 and tr_A0A1L9NAZ1_A0A1L9NAZ1_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G2YZC4_G2YZC4_BOTF4_999810 and tr_M7U1X4_M7U1X4_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SV09_F2SV09_TRIRC_559305 and tr_A0A178F8C2_A0A178F8C2_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G3Y351_G3Y351_ASPNA_380704 and tr_A0A319ARM9_A0A319ARM9_9EURO_1450533 are exactly identical! WARNING: Sequences tr_M4EEB3_M4EEB3_BRARP_51351 and tr_A0A078IZT0_A0A078IZT0_BRANA_3708 are exactly identical! WARNING: Sequences tr_W2PFI9_W2PFI9_PHYPN_761204 and tr_A0A0W8DK05_A0A0W8DK05_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A015N8S5_A0A015N8S5_9GLOM_1432141 and tr_A0A2H5TNY1_A0A2H5TNY1_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A087Y8L2_A0A087Y8L2_POEFO_48698 and tr_A0A087Y8S1_A0A087Y8S1_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A096NIF9_A0A096NIF9_PAPAN_9555 and tr_A0A2K5NZK5_A0A2K5NZK5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A078H9G8_A0A078H9G8_BRANA_3708 and tr_A0A0D3AAE3_A0A0D3AAE3_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094EWL8_A0A094EWL8_9PEZI_1420912 and tr_A0A1B8GK22_A0A1B8GK22_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0G4PCU2_A0A0G4PCU2_PENCA_1429867 and tr_A0A1V6P3C1_A0A1V6P3C1_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A0V1CPH9_A0A0V1CPH9_TRIBR_45882 and tr_A0A0V0UAF8_A0A0V0UAF8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0X2N7_A0A0V0X2N7_9BILA_92179 and tr_A0A0V1L451_A0A0V1L451_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A164W2S6_A0A164W2S6_9HOMO_1314777 and tr_A0A166D6I4_A0A166D6I4_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1V8UZ57_A0A1V8UZ57_9PEZI_1974281 and tr_A0A1V8SMZ0_A0A1V8SMZ0_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A2H3CRA5_A0A2H3CRA5_9AGAR_1076256 and tr_A0A284R6P9_A0A284R6P9_9AGAR_47428 are exactly identical! WARNING: Duplicate sequences found: 40 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O15160/4_raxmlng_ancestral/O15160.raxml.reduced.phy Alignment comprises 1 partitions and 346 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 346 Gaps: 7.87 % Invariant sites: 0.58 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O15160/4_raxmlng_ancestral/O15160.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/030621_run/phylogeny-snakemake/results/O15160/3_mltree/O15160.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 87 / 6960 [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: -182197.486469 [00:00:00 -182197.486469] Initial branch length optimization [00:00:01 -182041.214487] Model parameter optimization (eps = 0.100000) [00:00:45] Tree #1, final logLikelihood: -181635.441037 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.163278,0.286412) (0.272338,0.420197) (0.269020,0.945194) (0.295364,1.978992) 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/030621_run/phylogeny-snakemake/results/O15160/4_raxmlng_ancestral/O15160.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O15160/4_raxmlng_ancestral/O15160.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O15160/4_raxmlng_ancestral/O15160.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O15160/4_raxmlng_ancestral/O15160.raxml.log Analysis started: 23-Jun-2021 00:27:41 / finished: 23-Jun-2021 00:28:31 Elapsed time: 49.651 seconds Consumed energy: 3.505 Wh