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 01:42:14 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y276/2_msa/Q9Y276_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y276/3_mltree/Q9Y276.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y276/4_raxmlng_ancestral/Q9Y276 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622673734 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/Q9Y276/2_msa/Q9Y276_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 419 sites WARNING: Sequences tr_Q9VL22_Q9VL22_DROME_7227 and tr_B4HWH6_B4HWH6_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A2I3HGS0_A0A2I3HGS0_NOMLE_61853 and tr_A0A2J8TU41_A0A2J8TU41_PONAB_9601 are exactly identical! WARNING: Sequences tr_B6Q5F4_B6Q5F4_TALMQ_441960 and tr_A0A093XZF6_A0A093XZF6_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WDV5_B2WDV5_PYRTR_426418 and tr_A0A2W1EF80_A0A2W1EF80_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3QHN5_G3QHN5_GORGO_9595 and tr_H2R1H7_H2R1H7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QHN5_G3QHN5_GORGO_9595 and sp_Q9Y276_BCS1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QHN5_G3QHN5_GORGO_9595 and tr_A0A2R9A9U2_A0A2R9A9U2_PANPA_9597 are exactly identical! WARNING: Sequences tr_C0NW15_C0NW15_AJECG_447093 and tr_A6R8I5_A6R8I5_AJECN_339724 are exactly identical! WARNING: Sequences tr_Q7SGT9_Q7SGT9_NEUCR_367110 and tr_G4U6Q0_G4U6Q0_NEUT9_510952 are exactly identical! WARNING: Sequences tr_Q29NI5_Q29NI5_DROPS_46245 and tr_B4G799_B4G799_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8N541_B8N541_ASPFN_332952 and tr_Q2UBX1_Q2UBX1_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N541_B8N541_ASPFN_332952 and tr_A0A1S9DR32_A0A1S9DR32_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_F9FNY9_F9FNY9_FUSOF_660025 and tr_A0A0D2XPT7_A0A0D2XPT7_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FNY9_F9FNY9_FUSOF_660025 and tr_X0C057_X0C057_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FNY9_F9FNY9_FUSOF_660025 and tr_A0A2H3TDC8_A0A2H3TDC8_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FNY9_F9FNY9_FUSOF_660025 and tr_A0A2H3HN54_A0A2H3HN54_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9G2R4_F9G2R4_FUSOF_660025 and tr_X0C8P8_X0C8P8_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9G2R4_F9G2R4_FUSOF_660025 and tr_A0A2H3T6X6_A0A2H3T6X6_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9G2R4_F9G2R4_FUSOF_660025 and tr_A0A2H3HCY0_A0A2H3HCY0_FUSOX_327505 are exactly identical! WARNING: Sequences tr_A0A0H5S5R6_A0A0H5S5R6_BRUMA_6279 and tr_A0A0N4TTM6_A0A0N4TTM6_BRUPA_6280 are exactly identical! WARNING: Sequences tr_F7HF82_F7HF82_MACMU_9544 and tr_G7P2D1_G7P2D1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HF82_F7HF82_MACMU_9544 and tr_A0A096N224_A0A096N224_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HF82_F7HF82_MACMU_9544 and tr_A0A2K6CLG4_A0A2K6CLG4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7XBL2_G7XBL2_ASPKW_1033177 and tr_A0A100I8L4_A0A100I8L4_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XBL2_G7XBL2_ASPKW_1033177 and tr_A0A146FE46_A0A146FE46_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XBL2_G7XBL2_ASPKW_1033177 and tr_A0A1L9N7X8_A0A1L9N7X8_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7XBL2_G7XBL2_ASPKW_1033177 and tr_A0A317UX03_A0A317UX03_9EURO_1448314 are exactly identical! WARNING: Sequences tr_F9X2K5_F9X2K5_ZYMTI_336722 and tr_A0A0F4G782_A0A0F4G782_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_F9X2K5_F9X2K5_ZYMTI_336722 and tr_A0A1X7RIB4_A0A1X7RIB4_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F2SMK5_F2SMK5_TRIRC_559305 and tr_A0A178EPS9_A0A178EPS9_TRIRU_5551 are exactly identical! WARNING: Sequences tr_B3RWT7_B3RWT7_TRIAD_10228 and tr_A0A369SF31_A0A369SF31_9METZ_287889 are exactly identical! WARNING: Sequences tr_G3Y0S7_G3Y0S7_ASPNA_380704 and tr_A0A318ZT46_A0A318ZT46_9EURO_1450533 are exactly identical! WARNING: Sequences tr_S2JMU1_S2JMU1_MUCC1_1220926 and tr_A0A168NXF6_A0A168NXF6_MUCCL_747725 are exactly identical! WARNING: Sequences tr_V2WY41_V2WY41_MONRO_1381753 and tr_A0A0W0F538_A0A0W0F538_9AGAR_221103 are exactly identical! WARNING: Sequences tr_V2XP20_V2XP20_MONRO_1381753 and tr_A0A0W0FL86_A0A0W0FL86_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A0F0IGR7_A0A0F0IGR7_ASPPU_1403190 and tr_A0A2G7FPP7_A0A2G7FPP7_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0F8V3C4_A0A0F8V3C4_9EURO_308745 and tr_A0A2T5LYS6_A0A2T5LYS6_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0A1NDW7_A0A0A1NDW7_9FUNG_58291 and tr_A0A367JM40_A0A367JM40_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0V1DC04_A0A0V1DC04_TRIBR_45882 and tr_A0A0V1P660_A0A0V1P660_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A166U7T8_A0A166U7T8_9PEZI_708197 and tr_A0A161YGK3_A0A161YGK3_9PEZI_1573173 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/020621_run/phylogeny-snakemake/results/Q9Y276/4_raxmlng_ancestral/Q9Y276.raxml.reduced.phy Alignment comprises 1 partitions and 419 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 419 Gaps: 6.48 % Invariant sites: 1.19 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y276/4_raxmlng_ancestral/Q9Y276.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/Q9Y276/3_mltree/Q9Y276.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 105 / 8400 [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: -215167.611716 [00:00:00 -215167.611716] Initial branch length optimization [00:00:01 -214652.433423] Model parameter optimization (eps = 0.100000) [00:00:28] Tree #1, final logLikelihood: -214231.418853 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.161059,0.228399) (0.261072,0.347727) (0.373600,1.000316) (0.204269,2.441461) 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/Q9Y276/4_raxmlng_ancestral/Q9Y276.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y276/4_raxmlng_ancestral/Q9Y276.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y276/4_raxmlng_ancestral/Q9Y276.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y276/4_raxmlng_ancestral/Q9Y276.raxml.log Analysis started: 03-Jun-2021 01:42:14 / finished: 03-Jun-2021 01:42:47 Elapsed time: 32.739 seconds Consumed energy: 1.706 Wh