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 13:33:21 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37275/2_msa/P37275_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37275/3_mltree/P37275.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37275/4_raxmlng_ancestral/P37275 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802801 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/P37275/2_msa/P37275_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1124 sites WARNING: Sequences tr_A0A2I2ZTG0_A0A2I2ZTG0_GORGO_9595 and sp_P17036_ZNF3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QQX3_G3QQX3_GORGO_9595 and tr_H2QV13_H2QV13_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QQX3_G3QQX3_GORGO_9595 and sp_P17029_ZKSC1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QQX3_G3QQX3_GORGO_9595 and tr_A0A2R9BHM6_A0A2R9BHM6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8RQJ6_A0A2J8RQJ6_PONAB_9601 and sp_O75467_Z324A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RDQ4_A0A2I3RDQ4_PANTR_9598 and tr_A0A2R9B9C8_A0A2R9B9C8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3RT74_A0A2I3RT74_PANTR_9598 and sp_Q8TAF7_ZN461_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RT74_A0A2I3RT74_PANTR_9598 and tr_A0A2R9CCR9_A0A2R9CCR9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SMZ0_A0A2I3SMZ0_PANTR_9598 and tr_A0A2R9CHC6_A0A2R9CHC6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TSX8_A0A2I3TSX8_PANTR_9598 and tr_A0A2R9C1J6_A0A2R9C1J6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TW56_A0A2I3TW56_PANTR_9598 and tr_A0A2R8ZVK3_A0A2R8ZVK3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QBZ7_H2QBZ7_PANTR_9598 and tr_A0A2R9BW24_A0A2R9BW24_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A087ZWL4_A0A087ZWL4_APIME_7460 and tr_A0A2A3E3M7_A0A2A3E3M7_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NPF2_A0A158NPF2_ATTCE_12957 and tr_A0A195B9A9_A0A195B9A9_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6SLB4_F6SLB4_MACMU_9544 and tr_G7PTA6_G7PTA6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6SLB4_F6SLB4_MACMU_9544 and tr_A0A2K6BGX0_A0A2K6BGX0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7C2Z5_F7C2Z5_MACMU_9544 and tr_A0A2R8M5G3_A0A2R8M5G3_CALJA_9483 are exactly identical! WARNING: Sequences tr_F7C2Z5_F7C2Z5_MACMU_9544 and tr_A0A0D9RUH7_A0A0D9RUH7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7C2Z5_F7C2Z5_MACMU_9544 and tr_A0A2K5N059_A0A2K5N059_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7C2Z5_F7C2Z5_MACMU_9544 and tr_A0A2K6D8C7_A0A2K6D8C7_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZNU3_H0ZNU3_TAEGU_59729 and tr_A0A091EXL2_A0A091EXL2_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZNU3_H0ZNU3_TAEGU_59729 and tr_A0A093QCP3_A0A093QCP3_9PASS_328815 are exactly identical! WARNING: Sequences tr_G7P0C3_G7P0C3_MACFA_9541 and tr_A0A2K6DHH7_A0A2K6DHH7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PZB3_G7PZB3_MACFA_9541 and tr_A0A2K6BZF6_A0A2K6BZF6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MQ78_A0A096MQ78_PAPAN_9555 and tr_A0A2K5ZGD5_A0A2K5ZGD5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MNS1_A0A2I3MNS1_PAPAN_9555 and tr_A0A2K5LAJ0_A0A2K5LAJ0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MNS1_A0A2I3MNS1_PAPAN_9555 and tr_A0A2K5Y6G8_A0A2K5Y6G8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091VXR5_A0A091VXR5_OPIHO_30419 and tr_A0A091G9Y2_A0A091G9Y2_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A2I0MG40_A0A2I0MG40_COLLI_8932 and tr_A0A1V4K5G6_A0A1V4K5G6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0V405_A0A0V0V405_9BILA_181606 and tr_A0A0V0ZXX6_A0A0V0ZXX6_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0V405_A0A0V0V405_9BILA_181606 and tr_A0A0V1PCE4_A0A0V1PCE4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0V405_A0A0V0V405_9BILA_181606 and tr_A0A0V0U694_A0A0V0U694_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1U7Q2B8_A0A1U7Q2B8_MESAU_10036 and sp_Q60542_ZEB1_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2D0S451_A0A2D0S451_ICTPU_7998 and tr_A0A2D0S453_A0A2D0S453_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S519_A0A2D0S519_ICTPU_7998 and tr_A0A2D0S5M9_A0A2D0S5M9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5N5Y3_A0A2K5N5Y3_CERAT_9531 and tr_A0A2K5XNG6_A0A2K5XNG6_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 36 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/P37275/4_raxmlng_ancestral/P37275.raxml.reduced.phy Alignment comprises 1 partitions and 1124 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1124 Gaps: 57.55 % Invariant sites: 0.09 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37275/4_raxmlng_ancestral/P37275.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/P37275/3_mltree/P37275.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 281 / 22480 [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: -312699.825525 [00:00:00 -312699.825525] Initial branch length optimization [00:00:03 -298713.458534] Model parameter optimization (eps = 0.100000) [00:03:05] Tree #1, final logLikelihood: -297740.732621 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.058765,0.166495) (0.054223,0.595345) (0.299358,0.562912) (0.587654,1.343346) 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/P37275/4_raxmlng_ancestral/P37275.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37275/4_raxmlng_ancestral/P37275.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37275/4_raxmlng_ancestral/P37275.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37275/4_raxmlng_ancestral/P37275.raxml.log Analysis started: 04-Jun-2021 13:33:21 / finished: 04-Jun-2021 13:36:44 Elapsed time: 203.133 seconds