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 12-Jul-2021 17:30:53 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96EQ8/2_msa/Q96EQ8_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96EQ8/3_mltree/Q96EQ8.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96EQ8/4_raxmlng_ancestral/Q96EQ8 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100253 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/Q96EQ8/2_msa/Q96EQ8_nogap_msa.fasta [00:00:00] Loaded alignment with 668 taxa and 232 sites WARNING: Sequences tr_F1NAX4_F1NAX4_CHICK_9031 and sp_Q5F3B2_RN166_CHICK_9031 are exactly identical! WARNING: Sequences sp_Q3U9F6_RN166_MOUSE_10090 and sp_Q6J1I7_RN166_RAT_10116 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_H2QBQ3_H2QBQ3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and sp_Q96A37_RN166_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_A0A096N2Q9_A0A096N2Q9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_A0A0D9S2C6_A0A0D9S2C6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_A0A2K5KVC0_A0A2K5KVC0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_A0A2K6E6Q7_A0A2K6E6Q7_MACNE_9545 are exactly identical! WARNING: Sequences tr_Q7SAR3_Q7SAR3_NEUCR_367110 and tr_G4UL05_G4UL05_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8ND94_B8ND94_ASPFN_332952 and tr_Q2U933_Q2U933_ASPOR_510516 are exactly identical! WARNING: Sequences tr_H2QAM1_H2QAM1_PANTR_9598 and sp_Q9NZS9_BFAR_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QAM1_H2QAM1_PANTR_9598 and tr_A0A2R9BGJ5_A0A2R9BGJ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QKK0_H2QKK0_PANTR_9598 and sp_Q9Y508_RN114_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QKK0_H2QKK0_PANTR_9598 and tr_A0A2R9CS64_A0A2R9CS64_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A368SPC2_A0A368SPC2_SETIT_4555 and tr_A0A2T7CB53_A0A2T7CB53_9POAL_1504633 are exactly identical! WARNING: Sequences tr_A0A158NCF3_A0A158NCF3_ATTCE_12957 and tr_A0A195BWA2_A0A195BWA2_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0E0GPJ4_A0A0E0GPJ4_ORYNI_4536 and tr_B8AKS0_B8AKS0_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GPJ4_A0A0E0GPJ4_ORYNI_4536 and tr_A0A0D3FKD7_A0A0D3FKD7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GPJ4_A0A0E0GPJ4_ORYNI_4536 and tr_A0A0D9Z9H3_A0A0D9Z9H3_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F6RK58_F6RK58_MACMU_9544 and tr_A0A2I3MR78_A0A2I3MR78_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6RK58_F6RK58_MACMU_9544 and tr_A0A2K5LAN2_A0A2K5LAN2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6RK58_F6RK58_MACMU_9544 and tr_A0A2K6DRT9_A0A2K6DRT9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6RK58_F6RK58_MACMU_9544 and tr_A0A2K5YBT3_A0A2K5YBT3_MANLE_9568 are exactly identical! WARNING: Sequences tr_K7F953_K7F953_PELSI_13735 and tr_A0A093HKQ5_A0A093HKQ5_STRCA_441894 are exactly identical! WARNING: Sequences tr_F9X9I4_F9X9I4_ZYMTI_336722 and tr_A0A1X7RRJ4_A0A1X7RRJ4_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_A0A015IFT9_A0A015IFT9_9GLOM_1432141 and tr_A0A2I1DUR9_A0A2I1DUR9_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015JUW3_A0A015JUW3_9GLOM_1432141 and tr_A0A2H5U8E4_A0A2H5U8E4_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A067EJW4_A0A067EJW4_CITSI_2711 and tr_A0A2H5QR41_A0A2H5QR41_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A078G3F8_A0A078G3F8_BRANA_3708 and tr_A0A0D3CBA6_A0A0D3CBA6_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0D9RZ49_A0A0D9RZ49_CHLSB_60711 and tr_A0A2K5NPG8_A0A2K5NPG8_CERAT_9531 are exactly identical! WARNING: Sequences tr_X0CA06_X0CA06_FUSOX_1089458 and tr_A0A2H3T9B8_A0A2H3T9B8_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A151N151_A0A151N151_ALLMI_8496 and tr_A0A3Q0GIB3_A0A3Q0GIB3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091F434_A0A091F434_CORBR_85066 and tr_A0A093QC98_A0A093QC98_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A087QQ40_A0A087QQ40_APTFO_9233 and tr_A0A0A0AUQ8_A0A0A0AUQ8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A226NC54_A0A226NC54_CALSU_9009 and tr_A0A226PEB3_A0A226PEB3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3V7P2_A0A2U3V7P2_TURTR_9739 and tr_A0A2Y9Q2B4_A0A2Y9Q2B4_DELLE_9749 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_300621/phylogeny-snakemake/results/Q96EQ8/4_raxmlng_ancestral/Q96EQ8.raxml.reduced.phy Alignment comprises 1 partitions and 232 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 232 Gaps: 27.25 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96EQ8/4_raxmlng_ancestral/Q96EQ8.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/Q96EQ8/3_mltree/Q96EQ8.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 58 / 4640 [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: -148140.228208 [00:00:00 -148140.228208] Initial branch length optimization [00:00:01 -92120.508039] Model parameter optimization (eps = 0.100000) [00:00:29] Tree #1, final logLikelihood: -92021.789298 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.060503,0.136484) (0.099298,0.444051) (0.420670,0.714206) (0.419528,1.542693) 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/Q96EQ8/4_raxmlng_ancestral/Q96EQ8.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96EQ8/4_raxmlng_ancestral/Q96EQ8.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96EQ8/4_raxmlng_ancestral/Q96EQ8.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96EQ8/4_raxmlng_ancestral/Q96EQ8.raxml.log Analysis started: 12-Jul-2021 17:30:53 / finished: 12-Jul-2021 17:31:25 Elapsed time: 31.366 seconds