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 12-Jul-2021 18:12:33 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P85298/2_msa/P85298_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P85298/3_mltree/P85298.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P85298/4_raxmlng_ancestral/P85298 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102753 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/300621_run/phylogeny-snakemake/results/P85298/2_msa/P85298_nogap_msa.fasta [00:00:00] Loaded alignment with 995 taxa and 464 sites WARNING: Sequences tr_B4QSS8_B4QSS8_DROSI_7240 and tr_B4IHQ7_B4IHQ7_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1RDK5_G1RDK5_NOMLE_61853 and tr_H2PDT8_H2PDT8_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RDK5_G1RDK5_NOMLE_61853 and tr_A0A2R9BLQ3_A0A2R9BLQ3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RR24_G3RR24_GORGO_9595 and tr_H2QPW1_H2QPW1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RR24_G3RR24_GORGO_9595 and sp_O94988_FA13A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A0R3P3H6_A0A0R3P3H6_DROPS_46245 and tr_B4GR62_B4GR62_DROPE_7234 are exactly identical! WARNING: Sequences tr_B5DPL4_B5DPL4_DROPS_46245 and tr_B4HBP4_B4HBP4_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q294C7_Q294C7_DROPS_46245 and tr_B4GL97_B4GL97_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A158ND88_A0A158ND88_ATTCE_12957 and tr_F4X764_F4X764_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A0H5S4P2_A0A0H5S4P2_BRUMA_6279 and tr_A0A0R3R2V4_A0A0R3R2V4_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A1D5QQF8_A0A1D5QQF8_MACMU_9544 and tr_A0A096NCP5_A0A096NCP5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QQF8_A0A1D5QQF8_MACMU_9544 and tr_A0A0D9S2M7_A0A0D9S2M7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QQF8_A0A1D5QQF8_MACMU_9544 and tr_A0A2K5MRP3_A0A2K5MRP3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QQF8_A0A1D5QQF8_MACMU_9544 and tr_A0A2K6DT65_A0A2K6DT65_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QQF8_A0A1D5QQF8_MACMU_9544 and tr_A0A2K6AB85_A0A2K6AB85_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6QXF1_F6QXF1_MACMU_9544 and tr_G7P5W9_G7P5W9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6T0E0_F6T0E0_MACMU_9544 and tr_G7PQA9_G7PQA9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6T0E0_F6T0E0_MACMU_9544 and tr_A0A2K6E3J3_A0A2K6E3J3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UV94_F6UV94_MACMU_9544 and tr_A0A096MUE0_A0A096MUE0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6UV94_F6UV94_MACMU_9544 and tr_A0A2K5MWD6_A0A2K5MWD6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6ZKA6_F6ZKA6_MACMU_9544 and tr_A0A2I3N343_A0A2I3N343_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6ZKA6_F6ZKA6_MACMU_9544 and tr_A0A2K5MYE2_A0A2K5MYE2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6ZKA6_F6ZKA6_MACMU_9544 and tr_A0A2K5YTJ0_A0A2K5YTJ0_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HAB5_F7HAB5_MACMU_9544 and tr_A0A096NJX1_A0A096NJX1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HAB5_F7HAB5_MACMU_9544 and tr_A0A2K5NI89_A0A2K5NI89_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HAB5_F7HAB5_MACMU_9544 and tr_A0A2K6ACK1_A0A2K6ACK1_MANLE_9568 are exactly identical! WARNING: Sequences tr_E3LF87_E3LF87_CAERE_31234 and tr_A0A260YSE8_A0A260YSE8_9PELO_1503980 are exactly identical! WARNING: Sequences tr_L0PEA9_L0PEA9_PNEJ8_1209962 and tr_A0A0W4ZWG2_A0A0W4ZWG2_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_V2XPN8_V2XPN8_MONRO_1381753 and tr_A0A0W0EV24_A0A0W0EV24_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A087YCU3_A0A087YCU3_POEFO_48698 and tr_A0A087YCV3_A0A087YCV3_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A096N0Q0_A0A096N0Q0_PAPAN_9555 and tr_A0A0D9QW48_A0A0D9QW48_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096N0Q0_A0A096N0Q0_PAPAN_9555 and tr_A0A2K5NDS4_A0A2K5NDS4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9R051_A0A0D9R051_CHLSB_60711 and tr_A0A2K5NY60_A0A2K5NY60_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9R051_A0A0D9R051_CHLSB_60711 and tr_A0A2K5YJ75_A0A2K5YJ75_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0V1L705_A0A0V1L705_9BILA_6335 and tr_A0A0V1P8X9_A0A0V1P8X9_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1L705_A0A0V1L705_9BILA_6335 and tr_A0A0V0TZE0_A0A0V0TZE0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0P1B9Q5_A0A0P1B9Q5_9BASI_401625 and tr_A0A316VW51_A0A316VW51_9BASI_1522189 are exactly identical! WARNING: Sequences tr_A0A195DJ22_A0A195DJ22_9HYME_471704 and tr_A0A195B186_A0A195B186_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A2D0T2F5_A0A2D0T2F5_ICTPU_7998 and tr_A0A2D0T2I7_A0A2D0T2I7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T2F5_A0A2D0T2F5_ICTPU_7998 and tr_A0A2D0T2R8_A0A2D0T2R8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T2U2_A0A2D0T2U2_ICTPU_7998 and tr_A0A2D0T3E0_A0A2D0T3E0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3XE97_A0A2U3XE97_LEPWE_9713 and tr_A0A384DBH2_A0A384DBH2_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 42 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P85298/4_raxmlng_ancestral/P85298.raxml.reduced.phy Alignment comprises 1 partitions and 464 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 464 Gaps: 32.87 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P85298/4_raxmlng_ancestral/P85298.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/300621_run/phylogeny-snakemake/results/P85298/3_mltree/P85298.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 116 / 9280 [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: -205813.192782 [00:00:00 -205813.192782] Initial branch length optimization [00:00:01 -192206.110585] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -191789.231067 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.078650,0.340799) (0.153182,0.391805) (0.367802,0.755371) (0.400366,1.586929) 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/300621_run/phylogeny-snakemake/results/P85298/4_raxmlng_ancestral/P85298.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P85298/4_raxmlng_ancestral/P85298.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P85298/4_raxmlng_ancestral/P85298.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P85298/4_raxmlng_ancestral/P85298.raxml.log Analysis started: 12-Jul-2021 18:12:33 / finished: 12-Jul-2021 18:13:19 Elapsed time: 46.175 seconds Consumed energy: 1.718 Wh