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 13:35:31 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04637/2_msa/Q04637_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04637/3_mltree/Q04637.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04637/4_raxmlng_ancestral/Q04637 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802931 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/Q04637/2_msa/Q04637_nogap_msa.fasta [00:00:00] Loaded alignment with 989 taxa and 1599 sites WARNING: Sequences tr_M3YN81_M3YN81_MUSPF_9669 and tr_A0A2I3FWW3_A0A2I3FWW3_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YN81_M3YN81_MUSPF_9669 and tr_F1S6V4_F1S6V4_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YN81_M3YN81_MUSPF_9669 and tr_G7PQQ4_G7PQQ4_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3YN81_M3YN81_MUSPF_9669 and tr_A0A0D9QX32_A0A0D9QX32_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YN81_M3YN81_MUSPF_9669 and tr_A0A2K5NFV5_A0A2K5NFV5_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YN81_M3YN81_MUSPF_9669 and tr_A0A2K6D124_A0A2K6D124_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YN81_M3YN81_MUSPF_9669 and tr_A0A2K5ZGN7_A0A2K5ZGN7_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YN81_M3YN81_MUSPF_9669 and tr_A0A2Y9L1E6_A0A2Y9L1E6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YN81_M3YN81_MUSPF_9669 and tr_A0A2Y9F634_A0A2Y9F634_PHYCD_9755 are exactly identical! WARNING: Sequences tr_J3K497_J3K497_COCIM_246410 and tr_A0A0J6YGM1_A0A0J6YGM1_COCIT_404692 are exactly identical! WARNING: Sequences tr_G3RB28_G3RB28_GORGO_9595 and tr_A0A2R9A802_A0A2R9A802_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5R7J9_IF4G2_PONAB_9601 and sp_P78344_IF4G2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5R7J9_IF4G2_PONAB_9601 and tr_F2Z4C6_F2Z4C6_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q5R7J9_IF4G2_PONAB_9601 and sp_Q95L46_IF4G2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F1PAH7_F1PAH7_CANLF_9615 and tr_G1M7U8_G1M7U8_AILME_9646 are exactly identical! WARNING: Sequences tr_F1PAH7_F1PAH7_CANLF_9615 and tr_A0A2Y9M237_A0A2Y9M237_DELLE_9749 are exactly identical! WARNING: Sequences tr_F1PAH7_F1PAH7_CANLF_9615 and tr_A0A384DTQ8_A0A384DTQ8_URSMA_29073 are exactly identical! WARNING: Sequences tr_F9G5B6_F9G5B6_FUSOF_660025 and tr_X0CL04_X0CL04_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_Q2TZU3_Q2TZU3_ASPOR_510516 and tr_A0A1S9DDF0_A0A1S9DDF0_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_G3TA50_G3TA50_LOXAF_9785 and tr_F7BSW0_F7BSW0_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3TA50_G3TA50_LOXAF_9785 and tr_M3WZN7_M3WZN7_FELCA_9685 are exactly identical! WARNING: Sequences tr_G7E0T6_G7E0T6_MIXOS_764103 and tr_G7E0T7_G7E0T7_MIXOS_764103 are exactly identical! WARNING: Sequences tr_W2Q3D8_W2Q3D8_PHYPN_761204 and tr_W2GMZ2_W2GMZ2_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A117E121_A0A117E121_ASPNG_5061 and tr_A0A1L9N454_A0A1L9N454_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A1S3YL73_A0A1S3YL73_TOBAC_4097 and tr_A0A1U7YH21_A0A1U7YH21_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3YU46_A0A1S3YU46_TOBAC_4097 and tr_A0A1U7X3H8_A0A1U7X3H8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CRP3_A0A1S4CRP3_TOBAC_4097 and tr_A0A1U7WZW5_A0A1U7WZW5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3V9F2_A0A1S3V9F2_VIGRR_3916 and tr_A0A3Q0FCX1_A0A3Q0FCX1_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A1S3V9F2_A0A1S3V9F2_VIGRR_3916 and tr_A0A3Q0FDR1_A0A3Q0FDR1_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A2D0SIU3_A0A2D0SIU3_ICTPU_7998 and tr_A0A2D0SIU6_A0A2D0SIU6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SIU3_A0A2D0SIU3_ICTPU_7998 and tr_A0A2D0SJF2_A0A2D0SJF2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T6Y6_A0A2D0T6Y6_ICTPU_7998 and tr_A0A2D0T6Z0_A0A2D0T6Z0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4CD92_A0A2U4CD92_TURTR_9739 and tr_A0A383ZJ91_A0A383ZJ91_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 33 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/Q04637/4_raxmlng_ancestral/Q04637.raxml.reduced.phy Alignment comprises 1 partitions and 1599 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1599 Gaps: 43.57 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04637/4_raxmlng_ancestral/Q04637.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/Q04637/3_mltree/Q04637.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 400 / 32000 [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: -701352.284024 [00:00:00 -701352.284024] Initial branch length optimization [00:00:04 -599057.612770] Model parameter optimization (eps = 0.100000) [00:02:03] Tree #1, final logLikelihood: -597592.559789 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.074161,0.283018) (0.069496,0.674503) (0.283452,0.568156) (0.572891,1.345964) 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/Q04637/4_raxmlng_ancestral/Q04637.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04637/4_raxmlng_ancestral/Q04637.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04637/4_raxmlng_ancestral/Q04637.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04637/4_raxmlng_ancestral/Q04637.raxml.log Analysis started: 04-Jun-2021 13:35:31 / finished: 04-Jun-2021 13:37:48 Elapsed time: 137.325 seconds