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) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 13:36:23 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P32298/2_msa/P32298_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P32298/3_mltree/P32298.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P32298/4_raxmlng_ancestral/P32298 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802983 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P32298/2_msa/P32298_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 578 sites WARNING: Sequences tr_B4QSM6_B4QSM6_DROSI_7240 and sp_P32866_GPRK2_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QSM6_B4QSM6_DROSI_7240 and tr_B4I027_B4I027_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A1D5PP79_A0A1D5PP79_CHICK_9031 and tr_H0ZB65_H0ZB65_TAEGU_59729 are exactly identical! WARNING: Sequences tr_A0A1D5PP79_A0A1D5PP79_CHICK_9031 and tr_A0A218V572_A0A218V572_9PASE_299123 are exactly identical! WARNING: Sequences tr_H2NCP1_H2NCP1_PONAB_9601 and tr_H2Q482_H2Q482_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NCP1_H2NCP1_PONAB_9601 and sp_P25098_ARBK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NCP1_H2NCP1_PONAB_9601 and tr_A0A096N611_A0A096N611_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2NCP1_H2NCP1_PONAB_9601 and tr_A0A0D9R809_A0A0D9R809_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2NCP1_H2NCP1_PONAB_9601 and tr_A0A2K5L0Z3_A0A2K5L0Z3_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2NCP1_H2NCP1_PONAB_9601 and tr_A0A2K6AR56_A0A2K6AR56_MACNE_9545 are exactly identical! WARNING: Sequences tr_Q29BB5_Q29BB5_DROPS_46245 and tr_B4GYT9_B4GYT9_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2Q7U6_H2Q7U6_PANTR_9598 and tr_A0A2R8ZIW3_A0A2R8ZIW3_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7B2K4_K7B2K4_PANTR_9598 and sp_P35626_ARBK2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7B2K4_K7B2K4_PANTR_9598 and tr_A0A0D9RCS3_A0A0D9RCS3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_K7B2K4_K7B2K4_PANTR_9598 and tr_A0A2K6BHH5_A0A2K6BHH5_MACNE_9545 are exactly identical! WARNING: Sequences tr_K7B2K4_K7B2K4_PANTR_9598 and tr_A0A2R9A3T4_A0A2R9A3T4_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7BG59_K7BG59_PANTR_9598 and tr_A0A2R9A0D5_A0A2R9A0D5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NFW2_A0A158NFW2_ATTCE_12957 and tr_A0A195E6Z4_A0A195E6Z4_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NFW2_A0A158NFW2_ATTCE_12957 and tr_A0A195B2L3_A0A195B2L3_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6SX33_F6SX33_MACMU_9544 and tr_A0A2K6B128_A0A2K6B128_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7E0C1_F7E0C1_MACMU_9544 and tr_G7P015_G7P015_MACFA_9541 are exactly identical! WARNING: Sequences tr_E3MMQ6_E3MMQ6_CAERE_31234 and tr_A0A261CPL9_A0A261CPL9_9PELO_1503980 are exactly identical! WARNING: Sequences tr_M3W092_M3W092_FELCA_9685 and tr_A0A2Y9JMQ3_A0A2Y9JMQ3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_U3K1T7_U3K1T7_FICAL_59894 and tr_A0A091ENH3_A0A091ENH3_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3K1T7_U3K1T7_FICAL_59894 and tr_A0A093QGV9_A0A093QGV9_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3IST7_U3IST7_ANAPL_8839 and tr_A0A091G3N7_A0A091G3N7_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A015IPQ3_A0A015IPQ3_9GLOM_1432141 and tr_U9UPL3_U9UPL3_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A096NTY7_A0A096NTY7_PAPAN_9555 and tr_A0A2K5L696_A0A2K5L696_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9R8V9_A0A0D9R8V9_CHLSB_60711 and tr_A0A2K5MXF0_A0A2K5MXF0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091UM58_A0A091UM58_NIPNI_128390 and tr_A0A087R8T8_A0A087R8T8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091WUH3_A0A091WUH3_NIPNI_128390 and tr_A0A099ZZL1_A0A099ZZL1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V0S7L4_A0A0V0S7L4_9BILA_6336 and tr_A0A0V1DGE5_A0A0V1DGE5_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0S7L4_A0A0V0S7L4_9BILA_6336 and tr_A0A0V0VYU3_A0A0V0VYU3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0S7L4_A0A0V0S7L4_9BILA_6336 and tr_A0A0V0ZRE6_A0A0V0ZRE6_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0S7L4_A0A0V0S7L4_9BILA_6336 and tr_A0A0V1NVT5_A0A0V1NVT5_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0S7L4_A0A0V0S7L4_9BILA_6336 and tr_A0A0V0TRZ5_A0A0V0TRZ5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1EVP4_A0A0V1EVP4_TRIPS_6337 and tr_A0A0V1MHY7_A0A0V1MHY7_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V1EVP4_A0A0V1EVP4_TRIPS_6337 and tr_A0A0V1I3Q2_A0A0V1I3Q2_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1U7Q2D0_A0A1U7Q2D0_MESAU_10036 and sp_Q64682_ARBK1_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A226MV43_A0A226MV43_CALSU_9009 and tr_A0A226PZV1_A0A226PZV1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226N183_A0A226N183_CALSU_9009 and tr_A0A226PLK4_A0A226PLK4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3DIR7_A0A2H3DIR7_ARMGA_47427 and tr_A0A284RKH8_A0A284RKH8_9AGAR_47428 are exactly identical! WARNING: Duplicate sequences found: 42 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P32298/4_raxmlng_ancestral/P32298.raxml.reduced.phy Alignment comprises 1 partitions and 578 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 578 Gaps: 12.42 % Invariant sites: 0.35 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P32298/4_raxmlng_ancestral/P32298.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P32298/3_mltree/P32298.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 145 / 11600 [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: -183975.946653 [00:00:00 -183975.946653] Initial branch length optimization [00:00:01 -181507.732117] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -181232.084080 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.187310,0.264626) (0.213519,0.423140) (0.331164,0.833081) (0.268007,2.179786) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P32298/4_raxmlng_ancestral/P32298.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P32298/4_raxmlng_ancestral/P32298.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P32298/4_raxmlng_ancestral/P32298.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P32298/4_raxmlng_ancestral/P32298.raxml.log Analysis started: 04-Jun-2021 13:36:23 / finished: 04-Jun-2021 13:37:09 Elapsed time: 46.313 seconds