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 13:48:35 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08499/2_msa/Q08499_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08499/3_mltree/Q08499.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08499/4_raxmlng_ancestral/Q08499 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803715 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/Q08499/2_msa/Q08499_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 809 sites WARNING: Sequences tr_G1S7A7_G1S7A7_NOMLE_61853 and tr_G3QZ83_G3QZ83_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S7A7_G1S7A7_NOMLE_61853 and tr_H2NHK2_H2NHK2_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2ZIK5_A0A2I2ZIK5_GORGO_9595 and tr_H2P816_H2P816_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3SYQ5_A0A2I3SYQ5_PANTR_9598 and tr_A0A2R9B9J2_A0A2R9B9J2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NNE0_A0A158NNE0_ATTCE_12957 and tr_F4WJP5_F4WJP5_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NNE0_A0A158NNE0_ATTCE_12957 and tr_A0A195AUW3_A0A195AUW3_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6QKI6_F6QKI6_MACMU_9544 and tr_G7NW27_G7NW27_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6QKI6_F6QKI6_MACMU_9544 and tr_A0A2I3MDK2_A0A2I3MDK2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6QKI6_F6QKI6_MACMU_9544 and tr_A0A2K6DQY6_A0A2K6DQY6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GN31_F7GN31_MACMU_9544 and tr_A0A2K6DEB8_A0A2K6DEB8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GZT2_F7GZT2_MACMU_9544 and tr_A0A2K5LDG4_A0A2K5LDG4_CERAT_9531 are exactly identical! WARNING: Sequences tr_H9FVG2_H9FVG2_MACMU_9544 and tr_A0A2I3N850_A0A2I3N850_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9FVG2_H9FVG2_MACMU_9544 and tr_A0A2K5MHU3_A0A2K5MHU3_CERAT_9531 are exactly identical! WARNING: Sequences tr_H9FVG2_H9FVG2_MACMU_9544 and tr_A0A2K6D490_A0A2K6D490_MACNE_9545 are exactly identical! WARNING: Sequences tr_H9FVG2_H9FVG2_MACMU_9544 and tr_A0A2K5Z169_A0A2K5Z169_MANLE_9568 are exactly identical! WARNING: Sequences tr_R0LI76_R0LI76_ANAPL_8839 and tr_A0A091JKX3_A0A091JKX3_EGRGA_188379 are exactly identical! WARNING: Sequences tr_R0LI76_R0LI76_ANAPL_8839 and tr_A0A093PVW7_A0A093PVW7_9PASS_328815 are exactly identical! WARNING: Sequences tr_R0LI76_R0LI76_ANAPL_8839 and tr_A0A087R6B8_A0A087R6B8_APTFO_9233 are exactly identical! WARNING: Sequences tr_R0LI76_R0LI76_ANAPL_8839 and tr_A0A0A0AC11_A0A0A0AC11_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I3NAB7_A0A2I3NAB7_PAPAN_9555 and tr_A0A2K5ZIN2_A0A2K5ZIN2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I0M599_A0A2I0M599_COLLI_8932 and tr_A0A1V4KRN8_A0A1V4KRN8_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0ZZL1_A0A0V0ZZL1_9BILA_990121 and tr_A0A0V1A0J3_A0A0V1A0J3_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A1S3KF58_A0A1S3KF58_LINUN_7574 and tr_A0A1S3KFW4_A0A1S3KFW4_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1D1UCL3_A0A1D1UCL3_RAMVA_947166 and tr_A0A1D1UG97_A0A1D1UG97_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A226NGA0_A0A226NGA0_CALSU_9009 and tr_A0A226PR46_A0A226PR46_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RTL4_A0A2D0RTL4_ICTPU_7998 and tr_W5UKU3_W5UKU3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RUP9_A0A2D0RUP9_ICTPU_7998 and tr_A0A2D0RUQ8_A0A2D0RUQ8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LMP9_A0A2K5LMP9_CERAT_9531 and tr_A0A2K5Z928_A0A2K5Z928_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5N4R6_A0A2K5N4R6_CERAT_9531 and tr_A0A2K5ZUQ2_A0A2K5ZUQ2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3VCW9_A0A2U3VCW9_ODORO_9708 and tr_A0A2U3X6B6_A0A2U3X6B6_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 30 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/Q08499/4_raxmlng_ancestral/Q08499.raxml.reduced.phy Alignment comprises 1 partitions and 809 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 809 Gaps: 36.69 % Invariant sites: 0.25 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08499/4_raxmlng_ancestral/Q08499.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/Q08499/3_mltree/Q08499.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 203 / 16240 [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: -243790.886930 [00:00:00 -243790.886930] Initial branch length optimization [00:00:02 -202270.050710] Model parameter optimization (eps = 0.100000) [00:01:45] Tree #1, final logLikelihood: -200167.239248 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.189721,0.229956) (0.137398,0.203537) (0.352900,0.457825) (0.319981,2.396518) 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/Q08499/4_raxmlng_ancestral/Q08499.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08499/4_raxmlng_ancestral/Q08499.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08499/4_raxmlng_ancestral/Q08499.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08499/4_raxmlng_ancestral/Q08499.raxml.log Analysis started: 04-Jun-2021 13:48:35 / finished: 04-Jun-2021 13:50:27 Elapsed time: 112.938 seconds