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 02-Jun-2021 22:43:48 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51788/2_msa/P51788_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51788/3_mltree/P51788.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51788/4_raxmlng_ancestral/P51788 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622663028 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/P51788/2_msa/P51788_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 898 sites WARNING: Sequences tr_E1C9F3_E1C9F3_CHICK_9031 and tr_G1MUE4_G1MUE4_MELGA_9103 are exactly identical! WARNING: Sequences sp_P51791_CLCN3_MOUSE_10090 and sp_P51792_CLCN3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q9VGH7_CLCN2_DROME_7227 and tr_B4HHW9_B4HHW9_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1R4F3_G1R4F3_NOMLE_61853 and tr_G3REC5_G3REC5_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R4F3_G1R4F3_NOMLE_61853 and tr_A0A2I3TDA6_A0A2I3TDA6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R4F3_G1R4F3_NOMLE_61853 and tr_A0A096N8D7_A0A096N8D7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R4F3_G1R4F3_NOMLE_61853 and tr_A0A2K5MD25_A0A2K5MD25_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R4F3_G1R4F3_NOMLE_61853 and tr_A0A2K5ZHI2_A0A2K5ZHI2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3H3C4_G3H3C4_CRIGR_10029 and tr_A0A1U7QB56_A0A1U7QB56_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3HQF6_G3HQF6_CRIGR_10029 and tr_A0A1U8CVV4_A0A1U8CVV4_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q5RBK4_CLCN5_PONAB_9601 and sp_P51795_CLCN5_HUMAN_9606 are exactly identical! WARNING: Sequences sp_O18894_CLCN3_RABIT_9986 and sp_P51790_CLCN3_HUMAN_9606 are exactly identical! WARNING: Sequences sp_O18894_CLCN3_RABIT_9986 and tr_A0A0D9S237_A0A0D9S237_CHLSB_60711 are exactly identical! WARNING: Sequences tr_Q2M106_Q2M106_DROPS_46245 and tr_B4GQU3_B4GQU3_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2QVJ5_H2QVJ5_PANTR_9598 and tr_A0A2R8ZSS9_A0A2R8ZSS9_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7B9J0_K7B9J0_PANTR_9598 and tr_A0A2R9AD48_A0A2R9AD48_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7C4U1_F7C4U1_HORSE_9796 and tr_H0UV02_H0UV02_CAVPO_10141 are exactly identical! WARNING: Sequences tr_F7C4U1_F7C4U1_HORSE_9796 and tr_A0A091DKQ5_A0A091DKQ5_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A158P2X7_A0A158P2X7_ATTCE_12957 and tr_A0A195BPF1_A0A195BPF1_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6QD86_F6QD86_MACMU_9544 and tr_G7NYZ6_G7NYZ6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6QD86_F6QD86_MACMU_9544 and tr_A0A2I3M671_A0A2I3M671_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6QD86_F6QD86_MACMU_9544 and tr_A0A2K5N3F2_A0A2K5N3F2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6QD86_F6QD86_MACMU_9544 and tr_A0A2K6BR48_A0A2K6BR48_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_G7Q2R0_G7Q2R0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_A0A096MKP6_A0A096MKP6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_A0A0D9RK29_A0A0D9RK29_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_A0A2K5M2N3_A0A2K5M2N3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_A0A2K6E3J7_A0A2K6E3J7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_A0A2K5XEP2_A0A2K5XEP2_MANLE_9568 are exactly identical! WARNING: Sequences tr_D2H8P8_D2H8P8_AILME_9646 and tr_A0A2U3VDL9_A0A2U3VDL9_ODORO_9708 are exactly identical! WARNING: Sequences tr_D2H8P8_D2H8P8_AILME_9646 and tr_A0A2Y9K8Q2_A0A2Y9K8Q2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_D2H8P8_D2H8P8_AILME_9646 and tr_A0A384BNL3_A0A384BNL3_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1M083_G1M083_AILME_9646 and tr_A0A384C1S5_A0A384C1S5_URSMA_29073 are exactly identical! WARNING: Sequences tr_U3KA51_U3KA51_FICAL_59894 and tr_R0L8M0_R0L8M0_ANAPL_8839 are exactly identical! WARNING: Sequences tr_W2PU10_W2PU10_PHYPN_761204 and tr_A0A0W8CUA7_A0A0W8CUA7_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A015KAL6_A0A015KAL6_9GLOM_1432141 and tr_A0A2H5R0S5_A0A2H5R0S5_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A151PAZ9_A0A151PAZ9_ALLMI_8496 and tr_A0A1U7RYP9_A0A1U7RYP9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A093PFB9_A0A093PFB9_9PASS_328815 and tr_A0A091X5E4_A0A091X5E4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A093PFB9_A0A093PFB9_9PASS_328815 and tr_A0A087QNU4_A0A087QNU4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A093PFB9_A0A093PFB9_9PASS_328815 and tr_A0A093GPZ7_A0A093GPZ7_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A093PFB9_A0A093PFB9_9PASS_328815 and tr_A0A091WI55_A0A091WI55_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A093PFB9_A0A093PFB9_9PASS_328815 and tr_A0A0A0B366_A0A0A0B366_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A093PFB9_A0A093PFB9_9PASS_328815 and tr_A0A093G618_A0A093G618_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A1I7UQA2_A0A1I7UQA2_9PELO_1561998 and tr_A0A1I7UQA3_A0A1I7UQA3_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2D0R9D5_A0A2D0R9D5_ICTPU_7998 and tr_A0A2D0RBE7_A0A2D0RBE7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R9E3_A0A2D0R9E3_ICTPU_7998 and tr_A0A2D0RAR1_A0A2D0RAR1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T1R0_A0A2D0T1R0_ICTPU_7998 and tr_W5UD41_W5UD41_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4C162_A0A2U4C162_TURTR_9739 and tr_A0A2Y9MB75_A0A2Y9MB75_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 48 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/P51788/4_raxmlng_ancestral/P51788.raxml.reduced.phy Alignment comprises 1 partitions and 898 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 898 Gaps: 27.25 % Invariant sites: 0.00 % NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51788/4_raxmlng_ancestral/P51788.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/P51788/3_mltree/P51788.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 225 / 18000 [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: -327358.320091 [00:00:00 -327358.320091] Initial branch length optimization [00:00:01 -325471.701593] Model parameter optimization (eps = 0.100000) [00:01:38] Tree #1, final logLikelihood: -324368.472812 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.174772,0.344950) (0.193194,0.397343) (0.332126,0.874599) (0.299909,1.908819) 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/P51788/4_raxmlng_ancestral/P51788.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51788/4_raxmlng_ancestral/P51788.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51788/4_raxmlng_ancestral/P51788.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51788/4_raxmlng_ancestral/P51788.raxml.log Analysis started: 02-Jun-2021 22:43:48 / finished: 02-Jun-2021 22:45:34 Elapsed time: 106.710 seconds