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 02-Jun-2021 15:08:25 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P52333/2_msa/P52333_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P52333/3_mltree/P52333.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P52333/4_raxmlng_ancestral/P52333 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622635705 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/P52333/2_msa/P52333_nogap_msa.fasta [00:00:00] Loaded alignment with 996 taxa and 1124 sites WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_A0A2I2Z667_A0A2I2Z667_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and sp_Q15303_ERBB4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_F7G3H1_F7G3H1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_A0A2K5NV86_A0A2K5NV86_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_A0A2K6DNJ0_A0A2K6DNJ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R096_G3R096_GORGO_9595 and tr_A0A2I3TMU8_A0A2I3TMU8_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N755_H2N755_PONAB_9601 and tr_H2PZ66_H2PZ66_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N755_H2N755_PONAB_9601 and sp_P23458_JAK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RF60_A0A2I3RF60_PANTR_9598 and tr_A0A2R9C6L4_A0A2R9C6L4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3RYF9_A0A2I3RYF9_PANTR_9598 and sp_P00533_EGFR_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3SYV7_A0A2I3SYV7_PANTR_9598 and tr_A0A2R8ZP32_A0A2R8ZP32_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8KTF6_A0A2J8KTF6_PANTR_9598 and tr_A0A2R9BI29_A0A2R9BI29_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7DJM0_K7DJM0_PANTR_9598 and tr_A0A2R9C656_A0A2R9C656_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q07912_ACK1_HUMAN_9606 and tr_F6SXS7_F6SXS7_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q07912_ACK1_HUMAN_9606 and tr_G7NZ43_G7NZ43_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6YLX1_F6YLX1_MACMU_9544 and tr_A0A2I3LGP0_A0A2I3LGP0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6YLX1_F6YLX1_MACMU_9544 and tr_A0A0D9S727_A0A0D9S727_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6YLX1_F6YLX1_MACMU_9544 and tr_A0A2K5ZKJ8_A0A2K5ZKJ8_MANLE_9568 are exactly identical! WARNING: Sequences sp_P55245_EGFR_MACMU_9544 and tr_A0A0D9RU37_A0A0D9RU37_CHLSB_60711 are exactly identical! WARNING: Sequences sp_P55245_EGFR_MACMU_9544 and tr_A0A2K6B1P2_A0A2K6B1P2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZH03_H0ZH03_TAEGU_59729 and tr_U3JYF1_U3JYF1_FICAL_59894 are exactly identical! WARNING: Sequences tr_F1SSQ9_F1SSQ9_PIG_9823 and tr_A0A2Y9SV06_A0A2Y9SV06_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A096MVJ9_A0A096MVJ9_PAPAN_9555 and tr_A0A2K5N7J8_A0A2K5N7J8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9S388_A0A0D9S388_CHLSB_60711 and tr_A0A2K5L4X8_A0A2K5L4X8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A087R5J3_A0A087R5J3_APTFO_9233 and tr_A0A091GP40_A0A091GP40_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A087R5J3_A0A087R5J3_APTFO_9233 and tr_A0A091HM34_A0A091HM34_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A1U7Q225_A0A1U7Q225_MESAU_10036 and sp_Q60553_ERBB2_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2D0T7Y0_A0A2D0T7Y0_ICTPU_7998 and tr_A0A2D0T8L0_A0A2D0T8L0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5NHQ0_A0A2K5NHQ0_CERAT_9531 and tr_A0A2K6ARR6_A0A2K6ARR6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2U4B0F7_A0A2U4B0F7_TURTR_9739 and tr_A0A2Y9Q6T4_A0A2Y9Q6T4_DELLE_9749 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/P52333/4_raxmlng_ancestral/P52333.raxml.reduced.phy Alignment comprises 1 partitions and 1124 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1124 Gaps: 36.96 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P52333/4_raxmlng_ancestral/P52333.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/P52333/3_mltree/P52333.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 281 / 22480 [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: -321567.998888 [00:00:00 -321567.998888] Initial branch length optimization [00:00:02 -303493.864945] Model parameter optimization (eps = 0.100000) [00:01:09] Tree #1, final logLikelihood: -302738.153526 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.126625,0.290680) (0.116627,0.376229) (0.396248,0.774891) (0.360500,1.698378) 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/P52333/4_raxmlng_ancestral/P52333.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P52333/4_raxmlng_ancestral/P52333.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P52333/4_raxmlng_ancestral/P52333.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P52333/4_raxmlng_ancestral/P52333.raxml.log Analysis started: 02-Jun-2021 15:08:25 / finished: 02-Jun-2021 15:09:44 Elapsed time: 79.276 seconds