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 02:18:02 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P33897/2_msa/P33897_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P33897/3_mltree/P33897.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P33897/4_raxmlng_ancestral/P33897 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622675882 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/P33897/2_msa/P33897_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 745 sites WARNING: Sequences tr_B6QCP9_B6QCP9_TALMQ_441960 and tr_A0A093UMX1_A0A093UMX1_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2W7N6_B2W7N6_PYRTR_426418 and tr_A0A2W1GWS8_A0A2W1GWS8_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3R213_G3R213_GORGO_9595 and tr_H2Q5Q0_H2Q5Q0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R213_G3R213_GORGO_9595 and tr_A0A2R9ADA4_A0A2R9ADA4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SJ41_G3SJ41_GORGO_9595 and sp_P28288_ABCD3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SJ41_G3SJ41_GORGO_9595 and tr_A0A2R9BW79_A0A2R9BW79_PANPA_9597 are exactly identical! WARNING: Sequences tr_G2XBX1_G2XBX1_VERDV_498257 and tr_A0A0G4KVQ6_A0A0G4KVQ6_9PEZI_100787 are exactly identical! WARNING: Sequences tr_Q7SD69_Q7SD69_NEUCR_367110 and tr_G4U5C9_G4U5C9_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8N692_B8N692_ASPFN_332952 and tr_Q2UCG2_Q2UCG2_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N692_B8N692_ASPFN_332952 and tr_A0A2G7G8G3_A0A2G7G8G3_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179V5S2_A0A179V5S2_BLAGS_559298 and tr_C5GCS0_C5GCS0_AJEDR_559297 are exactly identical! WARNING: Sequences tr_E9ERE1_E9ERE1_METRA_655844 and tr_A0A0D9P7Y8_A0A0D9P7Y8_METAN_1291518 are exactly identical! WARNING: Sequences tr_J5JYS9_J5JYS9_BEAB2_655819 and tr_A0A0A2VSJ5_A0A0A2VSJ5_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J5JYS9_J5JYS9_BEAB2_655819 and tr_A0A2N6NTK9_A0A2N6NTK9_BEABA_176275 are exactly identical! WARNING: Sequences tr_A2QRE9_A2QRE9_ASPNC_425011 and tr_G3YHF0_G3YHF0_ASPNA_380704 are exactly identical! WARNING: Sequences tr_G7XNF6_G7XNF6_ASPKW_1033177 and tr_A0A100IJ55_A0A100IJ55_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G2YD36_G2YD36_BOTF4_999810 and tr_M7UT35_M7UT35_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_B4MF35_B4MF35_DROVI_7244 and tr_D0Z7D6_D0Z7D6_DROVI_7244 are exactly identical! WARNING: Sequences tr_F2SP79_F2SP79_TRIRC_559305 and tr_A0A178F4H0_A0A178F4H0_TRIRU_5551 are exactly identical! WARNING: Sequences tr_B3RUL2_B3RUL2_TRIAD_10228 and tr_A0A369S7L3_A0A369S7L3_9METZ_287889 are exactly identical! WARNING: Sequences tr_W7MFG1_W7MFG1_GIBM7_334819 and tr_A0A2K0W9U9_A0A2K0W9U9_GIBNY_42673 are exactly identical! WARNING: Sequences tr_S0DI77_S0DI77_GIBF5_1279085 and tr_N4UBE7_N4UBE7_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_S0DI77_S0DI77_GIBF5_1279085 and tr_X0DH18_X0DH18_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_S0DI77_S0DI77_GIBF5_1279085 and tr_A0A2H3SVU3_A0A2H3SVU3_FUSOX_5507 are exactly identical! WARNING: Sequences tr_S0DI77_S0DI77_GIBF5_1279085 and tr_A0A2H3I040_A0A2H3I040_FUSOX_327505 are exactly identical! WARNING: Sequences tr_S0DI77_S0DI77_GIBF5_1279085 and tr_A0A365MS63_A0A365MS63_GIBIN_948311 are exactly identical! WARNING: Sequences tr_N4U0K5_N4U0K5_FUSC1_1229664 and tr_X0DRQ2_X0DRQ2_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_N4U0K5_N4U0K5_FUSC1_1229664 and tr_A0A2H3T0U0_A0A2H3T0U0_FUSOX_5507 are exactly identical! WARNING: Sequences tr_U5H8L5_U5H8L5_USTV1_683840 and tr_A0A2X0MKK5_A0A2X0MKK5_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2WSG0_V2WSG0_MONRO_1381753 and tr_A0A0W0FPA4_A0A0W0FPA4_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2RES1_W2RES1_PHYPN_761204 and tr_A0A0W8D104_A0A0W8D104_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2RES1_W2RES1_PHYPN_761204 and tr_W2P7H7_W2P7H7_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A096NPC4_A0A096NPC4_PAPAN_9555 and tr_A0A2K5MK07_A0A2K5MK07_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NPC4_A0A096NPC4_PAPAN_9555 and tr_A0A2K6C123_A0A2K6C123_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A094EF74_A0A094EF74_9PEZI_1420912 and tr_A0A1B8G7Y9_A0A1B8G7Y9_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094EL48_A0A094EL48_9PEZI_1420912 and tr_A0A1B8G8W8_A0A1B8G8W8_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F8UMX8_A0A0F8UMX8_9EURO_308745 and tr_A0A2T5M2L3_A0A2T5M2L3_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A1I7V4M4_A0A1I7V4M4_9PELO_1561998 and tr_A0A1I7V4M5_A0A1I7V4M5_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2H3C5K2_A0A2H3C5K2_9AGAR_1076256 and tr_A0A284RAL7_A0A284RAL7_9AGAR_47428 are exactly identical! WARNING: Duplicate sequences found: 39 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/P33897/4_raxmlng_ancestral/P33897.raxml.reduced.phy Alignment comprises 1 partitions and 745 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 745 Gaps: 11.74 % Invariant sites: 0.27 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P33897/4_raxmlng_ancestral/P33897.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/P33897/3_mltree/P33897.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 187 / 14960 [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: -247166.951515 [00:00:00 -247166.951515] Initial branch length optimization [00:00:01 -246501.468735] Model parameter optimization (eps = 0.100000) [00:00:35] Tree #1, final logLikelihood: -245620.345626 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.223662,0.246198) (0.274532,0.344889) (0.312167,1.142903) (0.189640,2.602178) 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/P33897/4_raxmlng_ancestral/P33897.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P33897/4_raxmlng_ancestral/P33897.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P33897/4_raxmlng_ancestral/P33897.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P33897/4_raxmlng_ancestral/P33897.raxml.log Analysis started: 03-Jun-2021 02:18:02 / finished: 03-Jun-2021 02:18:44 Elapsed time: 42.381 seconds Consumed energy: 2.075 Wh