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 02:14:25 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05166/2_msa/P05166_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05166/3_mltree/P05166.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05166/4_raxmlng_ancestral/P05166 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622675665 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/P05166/2_msa/P05166_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 539 sites WARNING: Sequences tr_B4QDC4_B4QDC4_DROSI_7240 and tr_B4HQB5_B4HQB5_DROSE_7238 are exactly identical! WARNING: Sequences tr_J3K8S0_J3K8S0_COCIM_246410 and tr_A0A0J6YAQ0_A0A0J6YAQ0_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2VUZ5_B2VUZ5_PYRTR_426418 and tr_A0A2W1EQM7_A0A2W1EQM7_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B2W988_B2W988_PYRTR_426418 and tr_A0A2W1E468_A0A2W1E468_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A2I3RUA8_A0A2I3RUA8_PANTR_9598 and tr_A0A2R9BP68_A0A2R9BP68_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QR16_H2QR16_PANTR_9598 and tr_A0A2R9CTB8_A0A2R9CTB8_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q2U451_Q2U451_ASPOR_510516 and tr_A0A1S9DHE3_A0A1S9DHE3_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A2QN36_A2QN36_ASPNC_425011 and tr_A0A319AR02_A0A319AR02_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A2R563_A2R563_ASPNC_425011 and tr_G3XXZ3_G3XXZ3_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2R563_A2R563_ASPNC_425011 and tr_A0A319AAU3_A0A319AAU3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7MJQ2_G7MJQ2_MACMU_9544 and tr_G7NXX6_G7NXX6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MJQ2_G7MJQ2_MACMU_9544 and tr_A0A2I3LLJ1_A0A2I3LLJ1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7MJQ2_G7MJQ2_MACMU_9544 and tr_A0A2K6B7E1_A0A2K6B7E1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7XH31_G7XH31_ASPKW_1033177 and tr_A0A146F1Z5_A0A146F1Z5_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XUA2_G7XUA2_ASPKW_1033177 and tr_A0A146FVC9_A0A146FVC9_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F4NS36_F4NS36_BATDJ_684364 and tr_A0A177WB07_A0A177WB07_BATDE_403673 are exactly identical! WARNING: Sequences tr_F9XD31_F9XD31_ZYMTI_336722 and tr_A0A1X7RWH6_A0A1X7RWH6_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2XNR2_G2XNR2_BOTF4_999810 and tr_M7UFV2_M7UFV2_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_G2Y766_G2Y766_BOTF4_999810 and tr_M7TMI2_M7TMI2_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_E3LCQ0_E3LCQ0_CAERE_31234 and tr_A0A261CSQ3_A0A261CSQ3_9PELO_1503980 are exactly identical! WARNING: Sequences tr_F2SMY2_F2SMY2_TRIRC_559305 and tr_D4AXH0_D4AXH0_ARTBC_663331 are exactly identical! WARNING: Sequences tr_F2SMY2_F2SMY2_TRIRC_559305 and tr_A0A178F317_A0A178F317_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G3XYK9_G3XYK9_ASPNA_380704 and tr_A0A100IDZ2_A0A100IDZ2_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G3XYK9_G3XYK9_ASPNA_380704 and tr_A0A1L9MY30_A0A1L9MY30_ASPTU_767770 are exactly identical! WARNING: Sequences tr_N4TGS2_N4TGS2_FUSC1_1229664 and tr_X0CX02_X0CX02_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_N4TGS2_N4TGS2_FUSC1_1229664 and tr_A0A2H3TGR9_A0A2H3TGR9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_N4TGS2_N4TGS2_FUSC1_1229664 and tr_A0A2H3GZA4_A0A2H3GZA4_FUSOX_327505 are exactly identical! WARNING: Sequences tr_W2PV88_W2PV88_PHYPN_761204 and tr_W2IK26_W2IK26_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QKS8_W2QKS8_PHYPN_761204 and tr_A0A0W8DB41_A0A0W8DB41_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QKS8_W2QKS8_PHYPN_761204 and tr_W2LT22_W2LT22_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A084QS12_A0A084QS12_STAC4_1283841 and tr_A0A084RC61_A0A084RC61_STACH_1283842 are exactly identical! WARNING: Sequences tr_A0A094H9N7_A0A094H9N7_9PEZI_1420912 and tr_A0A2P2SYF0_A0A2P2SYF0_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0V1CUF5_A0A0V1CUF5_TRIBR_45882 and tr_A0A0V1PDB0_A0A0V1PDB0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CUF5_A0A0V1CUF5_TRIBR_45882 and tr_A0A0V0UCV9_A0A0V0UCV9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A100IGG0_A0A100IGG0_ASPNG_5061 and tr_A0A1L9MRV3_A0A1L9MRV3_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A166XBL6_A0A166XBL6_9PEZI_708197 and tr_A0A162NYT0_A0A162NYT0_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_A0A1S3Z2C6_A0A1S3Z2C6_TOBAC_4097 and tr_A0A1U7W645_A0A1U7W645_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1B8ASV2_A0A1B8ASV2_FUSPO_36050 and tr_A0A2L2T6F7_A0A2L2T6F7_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A226NCS3_A0A226NCS3_CALSU_9009 and tr_A0A226PTM6_A0A226PTM6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A1U8DZI7_A0A1U8DZI7_CAPAN_4072 and tr_A0A2G3BV85_A0A2G3BV85_CAPCH_80379 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/P05166/4_raxmlng_ancestral/P05166.raxml.reduced.phy Alignment comprises 1 partitions and 539 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 539 Gaps: 10.22 % Invariant sites: 1.30 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05166/4_raxmlng_ancestral/P05166.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/P05166/3_mltree/P05166.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 135 / 10800 [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: -185237.651089 [00:00:00 -185237.651089] Initial branch length optimization [00:00:01 -184041.080599] Model parameter optimization (eps = 0.100000) [00:00:40] Tree #1, final logLikelihood: -183291.727606 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.244368,0.311811) (0.334495,0.394230) (0.250867,1.110989) (0.170270,3.014188) 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/P05166/4_raxmlng_ancestral/P05166.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05166/4_raxmlng_ancestral/P05166.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05166/4_raxmlng_ancestral/P05166.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05166/4_raxmlng_ancestral/P05166.raxml.log Analysis started: 03-Jun-2021 02:14:25 / finished: 03-Jun-2021 02:15:11 Elapsed time: 45.909 seconds Consumed energy: 2.514 Wh