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 20-Jul-2021 20:26:20 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78411/2_msa/P78411_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78411/3_mltree/P78411.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78411/4_raxmlng_ancestral/P78411 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626801980 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_300621/phylogeny-snakemake/results/P78411/2_msa/P78411_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 483 sites WARNING: Sequences tr_Q9PU52_Q9PU52_CHICK_9031 and tr_A0A226P9W0_A0A226P9W0_COLVI_9014 are exactly identical! WARNING: Sequences tr_M3YGQ2_M3YGQ2_MUSPF_9669 and tr_A0A2Y9IG28_A0A2Y9IG28_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3RJD8_G3RJD8_GORGO_9595 and tr_H2Q1S1_H2Q1S1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RJD8_G3RJD8_GORGO_9595 and sp_Q8IYA7_MKX_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RJD8_G3RJD8_GORGO_9595 and tr_A0A2R9C923_A0A2R9C923_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q2M0K9_Q2M0K9_DROPS_46245 and tr_B4GRH6_B4GRH6_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q2M0L1_Q2M0L1_DROPS_46245 and tr_B4GRH5_B4GRH5_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2QQL5_H2QQL5_PANTR_9598 and sp_Q9BZI1_IRX2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QQL6_H2QQL6_PANTR_9598 and sp_P78414_IRX1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F7H9D7_F7H9D7_MACMU_9544 and tr_A0A2K6BLC4_A0A2K6BLC4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HMJ3_F7HMJ3_MACMU_9544 and tr_A0A2K6DKG8_A0A2K6DKG8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1K3A9_G1K3A9_XENTR_8364 and sp_Q4LDQ3_IRX5_XENTR_8364 are exactly identical! WARNING: Sequences tr_G7PEN6_G7PEN6_MACFA_9541 and tr_A0A2I3LRS7_A0A2I3LRS7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PEN6_G7PEN6_MACFA_9541 and tr_A0A2K5L9B2_A0A2K5L9B2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PEN6_G7PEN6_MACFA_9541 and tr_A0A2K6DAN7_A0A2K6DAN7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PEN6_G7PEN6_MACFA_9541 and tr_A0A2K5X9L6_A0A2K5X9L6_MANLE_9568 are exactly identical! WARNING: Sequences tr_U3JXF9_U3JXF9_FICAL_59894 and tr_A0A218V672_A0A218V672_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3HYD2_U3HYD2_ANAPL_8839 and tr_A0A091F1M3_A0A091F1M3_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3HYD2_U3HYD2_ANAPL_8839 and tr_A0A091J5I4_A0A091J5I4_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3HYD2_U3HYD2_ANAPL_8839 and tr_A0A093PGA9_A0A093PGA9_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3HYD2_U3HYD2_ANAPL_8839 and tr_A0A087QX60_A0A087QX60_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3HYD2_U3HYD2_ANAPL_8839 and tr_A0A093HU92_A0A093HU92_STRCA_441894 are exactly identical! WARNING: Sequences tr_U3HYD2_U3HYD2_ANAPL_8839 and tr_A0A091VL91_A0A091VL91_OPIHO_30419 are exactly identical! WARNING: Sequences tr_U3HYD2_U3HYD2_ANAPL_8839 and tr_A0A099Z9W2_A0A099Z9W2_TINGU_94827 are exactly identical! WARNING: Sequences tr_U3HYD2_U3HYD2_ANAPL_8839 and tr_A0A091GIV9_A0A091GIV9_9AVES_55661 are exactly identical! WARNING: Sequences tr_U3HYD2_U3HYD2_ANAPL_8839 and tr_A0A093G833_A0A093G833_DRYPU_118200 are exactly identical! WARNING: Sequences tr_U3HYD2_U3HYD2_ANAPL_8839 and tr_A0A091IGK0_A0A091IGK0_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A096NEE5_A0A096NEE5_PAPAN_9555 and tr_A0A2K5LNQ6_A0A2K5LNQ6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NEE5_A0A096NEE5_PAPAN_9555 and tr_A0A2K6B9E6_A0A2K6B9E6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NIE7_A0A096NIE7_PAPAN_9555 and tr_A0A2K5P465_A0A2K5P465_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091EYR8_A0A091EYR8_CORBR_85066 and tr_A0A091VI45_A0A091VI45_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091EYR8_A0A091EYR8_CORBR_85066 and tr_A0A099Z4G8_A0A099Z4G8_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091EYR8_A0A091EYR8_CORBR_85066 and tr_A0A091FHL8_A0A091FHL8_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091EYR8_A0A091EYR8_CORBR_85066 and tr_A0A093G9S6_A0A093G9S6_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091EYR8_A0A091EYR8_CORBR_85066 and tr_A0A091HUZ8_A0A091HUZ8_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091F0Q3_A0A091F0Q3_CORBR_85066 and tr_A0A093PTG9_A0A093PTG9_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091F0Q3_A0A091F0Q3_CORBR_85066 and tr_A0A091G791_A0A091G791_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091F0Q3_A0A091F0Q3_CORBR_85066 and tr_A0A093GJJ6_A0A093GJJ6_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091F0Q3_A0A091F0Q3_CORBR_85066 and tr_A0A091IGV9_A0A091IGV9_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091FPB4_A0A091FPB4_CORBR_85066 and tr_A0A091J2Z3_A0A091J2Z3_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091FPB4_A0A091FPB4_CORBR_85066 and tr_A0A093RYW4_A0A093RYW4_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091FPB4_A0A091FPB4_CORBR_85066 and tr_A0A091VEQ4_A0A091VEQ4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091FPB4_A0A091FPB4_CORBR_85066 and tr_A0A087QX62_A0A087QX62_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091FPB4_A0A091FPB4_CORBR_85066 and tr_A0A091FY21_A0A091FY21_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091FPB4_A0A091FPB4_CORBR_85066 and tr_A0A0A0A0R7_A0A0A0A0R7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091FPB4_A0A091FPB4_CORBR_85066 and tr_A0A093GHF4_A0A093GHF4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091FPB4_A0A091FPB4_CORBR_85066 and tr_A0A091IDD5_A0A091IDD5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091G508_A0A091G508_9AVES_55661 and tr_A0A093GNL4_A0A093GNL4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A0V0SCD3_A0A0V0SCD3_9BILA_6336 and tr_A0A0V0V3X8_A0A0V0V3X8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A226N8E3_A0A226N8E3_CALSU_9009 and tr_A0A226P290_A0A226P290_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0SB76_A0A2D0SB76_ICTPU_7998 and tr_W5UK52_W5UK52_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T3R9_A0A2D0T3R9_ICTPU_7998 and tr_A0A2D0T405_A0A2D0T405_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 52 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78411/4_raxmlng_ancestral/P78411.raxml.reduced.phy Alignment comprises 1 partitions and 483 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 483 Gaps: 44.53 % Invariant sites: 0.21 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78411/4_raxmlng_ancestral/P78411.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_300621/phylogeny-snakemake/results/P78411/3_mltree/P78411.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 121 / 9680 [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: -677622.084647 [00:00:00 -677622.084647] Initial branch length optimization [00:00:03 -245199.664242] Model parameter optimization (eps = 0.100000) [00:00:57] Tree #1, final logLikelihood: -244392.435440 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.157487,0.197082) (0.133776,0.509407) (0.235421,0.674336) (0.473317,1.567794) 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_300621/phylogeny-snakemake/results/P78411/4_raxmlng_ancestral/P78411.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78411/4_raxmlng_ancestral/P78411.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78411/4_raxmlng_ancestral/P78411.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78411/4_raxmlng_ancestral/P78411.raxml.log Analysis started: 20-Jul-2021 20:26:20 / finished: 20-Jul-2021 20:27:21 Elapsed time: 61.490 seconds