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 03-Jun-2021 01:54:17 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P36551/2_msa/P36551_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P36551/3_mltree/P36551.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P36551/4_raxmlng_ancestral/P36551 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674457 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/P36551/2_msa/P36551_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 454 sites WARNING: Sequences tr_B2W2P7_B2W2P7_PYRTR_426418 and tr_A0A2W1GBP0_A0A2W1GBP0_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8PAX6_B8PAX6_POSPM_561896 and tr_A0A1X6MLK6_A0A1X6MLK6_9APHY_670580 are exactly identical! WARNING: Sequences tr_A0A179UV34_A0A179UV34_BLAGS_559298 and tr_C5GNP8_C5GNP8_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9FHU5_F9FHU5_FUSOF_660025 and tr_N4UC73_N4UC73_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FHU5_F9FHU5_FUSOF_660025 and tr_X0CFD4_X0CFD4_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FHU5_F9FHU5_FUSOF_660025 and tr_A0A2H3U2T7_A0A2H3U2T7_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FHU5_F9FHU5_FUSOF_660025 and tr_A0A365NPG8_A0A365NPG8_GIBIN_948311 are exactly identical! WARNING: Sequences tr_E9ERS9_E9ERS9_METRA_655844 and tr_A0A0B4IJI1_A0A0B4IJI1_METMF_1276143 are exactly identical! WARNING: Sequences tr_Q2UBH4_Q2UBH4_ASPOR_510516 and tr_A0A1S9DRZ5_A0A1S9DRZ5_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8AU70_B8AU70_ORYSI_39946 and tr_I1PPS9_I1PPS9_ORYGL_4538 are exactly identical! WARNING: Sequences tr_B8AU70_B8AU70_ORYSI_39946 and tr_A0A0E0PDX1_A0A0E0PDX1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_B8AU70_B8AU70_ORYSI_39946 and tr_A0A0D9ZQH8_A0A0D9ZQH8_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_B8AU70_B8AU70_ORYSI_39946 and sp_Q7XPL2_HEM6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G2Y7M5_G2Y7M5_BOTF4_999810 and tr_M7TRX6_M7TRX6_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A0A0R0G797_A0A0R0G797_SOYBN_3847 and sp_P35055_HEM6_SOYBN_3847 are exactly identical! WARNING: Sequences tr_F2SU30_F2SU30_TRIRC_559305 and tr_A0A178F6K2_A0A178F6K2_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G3XZT7_G3XZT7_ASPNA_380704 and tr_A0A319B0Z7_A0A319B0Z7_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A0A0D2Y8P8_A0A0D2Y8P8_FUSO4_426428 and tr_A0A2H3H138_A0A2H3H138_FUSOX_327505 are exactly identical! WARNING: Sequences tr_V2X4R0_V2X4R0_MONRO_1381753 and tr_A0A0W0G4Y1_A0A0W0G4Y1_9AGAR_221103 are exactly identical! WARNING: Sequences tr_V2X5N9_V2X5N9_MONRO_1381753 and tr_A0A0W0G4Y7_A0A0W0G4Y7_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2RE33_W2RE33_PHYPN_761204 and tr_A0A0W8DKC8_A0A0W8DKC8_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2RE33_W2RE33_PHYPN_761204 and tr_W2HS22_W2HS22_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2RG21_W2RG21_PHYPN_761204 and tr_A0A0W8DL68_A0A0W8DL68_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A067EH25_A0A067EH25_CITSI_2711 and tr_A0A2H5MX62_A0A2H5MX62_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0S7E048_A0A0S7E048_9EURO_293939 and tr_A0A2I1CAB0_A0A2I1CAB0_9EURO_1392255 are exactly identical! WARNING: Sequences tr_A0A0G4P6T4_A0A0G4P6T4_PENCA_1429867 and tr_A0A1V6NB94_A0A1V6NB94_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A100ICH3_A0A100ICH3_ASPNG_5061 and tr_A0A1L9MZH2_A0A1L9MZH2_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A146F3L0_A0A146F3L0_9EURO_1069201 and tr_A0A317W1D4_A0A317W1D4_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A1Q3E2M2_A0A1Q3E2M2_LENED_5353 and tr_A0A1Q3E316_A0A1Q3E316_LENED_5353 are exactly identical! WARNING: Sequences tr_A0A226MP76_A0A226MP76_CALSU_9009 and tr_A0A226PV86_A0A226PV86_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A1U8EMR2_A0A1U8EMR2_CAPAN_4072 and tr_A0A2G3BDP1_A0A2G3BDP1_CAPCH_80379 are exactly identical! WARNING: Duplicate sequences found: 31 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/P36551/4_raxmlng_ancestral/P36551.raxml.reduced.phy Alignment comprises 1 partitions and 454 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 454 Gaps: 25.36 % Invariant sites: 0.44 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P36551/4_raxmlng_ancestral/P36551.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/P36551/3_mltree/P36551.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 114 / 9120 [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: -188651.763119 [00:00:00 -188651.763119] Initial branch length optimization [00:00:01 -185986.286802] Model parameter optimization (eps = 0.100000) [00:00:31] Tree #1, final logLikelihood: -185535.891601 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.132960,0.230514) (0.270683,0.304267) (0.202564,0.836058) (0.393793,1.822367) 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/P36551/4_raxmlng_ancestral/P36551.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P36551/4_raxmlng_ancestral/P36551.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P36551/4_raxmlng_ancestral/P36551.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P36551/4_raxmlng_ancestral/P36551.raxml.log Analysis started: 03-Jun-2021 01:54:17 / finished: 03-Jun-2021 01:54:52 Elapsed time: 35.726 seconds Consumed energy: 2.058 Wh