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 17-Jul-2021 07:16:49 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75398/2_msa/O75398_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75398/3_mltree/O75398.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75398/4_raxmlng_ancestral/O75398 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626495409 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/O75398/2_msa/O75398_nogap_msa.fasta [00:00:00] Loaded alignment with 696 taxa and 565 sites WARNING: Sequences tr_A0A1D5PBA3_A0A1D5PBA3_CHICK_9031 and tr_G1NHB1_G1NHB1_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5PBA3_A0A1D5PBA3_CHICK_9031 and tr_R0JWE5_R0JWE5_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1D5PBA3_A0A1D5PBA3_CHICK_9031 and tr_A0A2I0MWV7_A0A2I0MWV7_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5PBA3_A0A1D5PBA3_CHICK_9031 and tr_A0A1V4KGU2_A0A1V4KGU2_PATFA_372326 are exactly identical! WARNING: Sequences tr_M3YCJ6_M3YCJ6_MUSPF_9669 and tr_F1PRY7_F1PRY7_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YCJ6_M3YCJ6_MUSPF_9669 and tr_A0A287D4Y6_A0A287D4Y6_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YCJ6_M3YCJ6_MUSPF_9669 and tr_A0A286XDD1_A0A286XDD1_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3YCJ6_M3YCJ6_MUSPF_9669 and sp_Q06455_MTG8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YCJ6_M3YCJ6_MUSPF_9669 and tr_G3SWV9_G3SWV9_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3YCJ6_M3YCJ6_MUSPF_9669 and tr_G1LKK1_G1LKK1_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YCJ6_M3YCJ6_MUSPF_9669 and tr_A0A1S3EX63_A0A1S3EX63_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3YCJ6_M3YCJ6_MUSPF_9669 and tr_A0A1U7ULE7_A0A1U7ULE7_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3YCJ6_M3YCJ6_MUSPF_9669 and tr_A0A2U3WXQ4_A0A2U3WXQ4_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YCJ6_M3YCJ6_MUSPF_9669 and tr_A0A2Y9JDV7_A0A2Y9JDV7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z2A8_M3Z2A8_MUSPF_9669 and tr_A0A2Y9IRS0_A0A2Y9IRS0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1P2T0_G1P2T0_MYOLU_59463 and tr_A0A2J8UG28_A0A2J8UG28_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1P2T0_G1P2T0_MYOLU_59463 and tr_A0A384BXQ6_A0A384BXQ6_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I2ZTU5_A0A2I2ZTU5_GORGO_9595 and tr_A0A2I3SDR0_A0A2I3SDR0_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZTU5_A0A2I2ZTU5_GORGO_9595 and tr_A0A2R9APX5_A0A2R9APX5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TQP7_A0A2I3TQP7_PANTR_9598 and tr_A0A2R9CEL1_A0A2R9CEL1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0G2K0G0_A0A0G2K0G0_RAT_10116 and tr_A0A3Q0CLU4_A0A3Q0CLU4_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A087ZS71_A0A087ZS71_APIME_7460 and tr_A0A2A3EPJ8_A0A2A3EPJ8_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NNI0_A0A158NNI0_ATTCE_12957 and tr_A0A151X7S9_A0A151X7S9_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NNI0_A0A158NNI0_ATTCE_12957 and tr_A0A151I3R2_A0A151I3R2_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A1D5QY91_A0A1D5QY91_MACMU_9544 and tr_A0A2I3MRP8_A0A2I3MRP8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QY91_A0A1D5QY91_MACMU_9544 and tr_A0A2K6DQW6_A0A2K6DQW6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QY91_A0A1D5QY91_MACMU_9544 and tr_A0A2K5Z1C9_A0A2K5Z1C9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A287A9Z0_A0A287A9Z0_PIG_9823 and tr_A0A2U4AI98_A0A2U4AI98_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A287A9Z0_A0A287A9Z0_PIG_9823 and tr_A0A2Y9RYY0_A0A2Y9RYY0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A091J3F9_A0A091J3F9_EGRGA_188379 and tr_A0A091VE88_A0A091VE88_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091J3F9_A0A091J3F9_EGRGA_188379 and tr_A0A093HJN5_A0A093HJN5_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091J3F9_A0A091J3F9_EGRGA_188379 and tr_A0A091WQ18_A0A091WQ18_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091J3F9_A0A091J3F9_EGRGA_188379 and tr_A0A0A0AYZ4_A0A0A0AYZ4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091J3F9_A0A091J3F9_EGRGA_188379 and tr_A0A093GQB7_A0A093GQB7_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091FU61_A0A091FU61_9AVES_55661 and tr_A0A091IGX0_A0A091IGX0_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A1S3JUG8_A0A1S3JUG8_LINUN_7574 and tr_A0A1S3JVC9_A0A1S3JVC9_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A2D0S5A7_A0A2D0S5A7_ICTPU_7998 and tr_A0A2D0S665_A0A2D0S665_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SCL5_A0A2D0SCL5_ICTPU_7998 and tr_A0A2D0SCL8_A0A2D0SCL8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2Y9PB52_A0A2Y9PB52_DELLE_9749 and tr_A0A383ZR00_A0A383ZR00_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 39 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/O75398/4_raxmlng_ancestral/O75398.raxml.reduced.phy Alignment comprises 1 partitions and 565 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 565 Gaps: 47.36 % Invariant sites: 0.18 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75398/4_raxmlng_ancestral/O75398.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/O75398/3_mltree/O75398.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 142 / 11360 [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: -143485.192197 [00:00:00 -143485.192197] Initial branch length optimization [00:00:01 -124021.604928] Model parameter optimization (eps = 0.100000) [00:00:40] Tree #1, final logLikelihood: -123501.567509 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.071745,0.317350) (0.073569,1.421044) (0.358311,0.610694) (0.496376,1.317287) 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/O75398/4_raxmlng_ancestral/O75398.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75398/4_raxmlng_ancestral/O75398.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75398/4_raxmlng_ancestral/O75398.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75398/4_raxmlng_ancestral/O75398.raxml.log Analysis started: 17-Jul-2021 07:16:49 / finished: 17-Jul-2021 07:17:34 Elapsed time: 44.115 seconds