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 13:39:37 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P27918/2_msa/P27918_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P27918/3_mltree/P27918.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P27918/4_raxmlng_ancestral/P27918 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803177 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/P27918/2_msa/P27918_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 469 sites WARNING: Sequences tr_M3YA63_M3YA63_MUSPF_9669 and tr_A0A2Y9LBU2_A0A2Y9LBU2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1QI60_G1QI60_NOMLE_61853 and tr_A0A2I2ZXA9_A0A2I2ZXA9_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QI60_G1QI60_NOMLE_61853 and tr_H9FXR7_H9FXR7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QI60_G1QI60_NOMLE_61853 and tr_A0A2K6C9T2_A0A2K6C9T2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1NWL5_G1NWL5_MYOLU_59463 and tr_G3T893_G3T893_LOXAF_9785 are exactly identical! WARNING: Sequences tr_A0A2I2ZS38_A0A2I2ZS38_GORGO_9595 and tr_A0A2I3RP89_A0A2I3RP89_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZS38_A0A2I2ZS38_GORGO_9595 and sp_P07996_TSP1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZS38_A0A2I2ZS38_GORGO_9595 and tr_A0A2R8ZKW5_A0A2R8ZKW5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R724_G3R724_GORGO_9595 and tr_H2QQM4_H2QQM4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R724_G3R724_GORGO_9595 and sp_Q13591_SEM5A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R724_G3R724_GORGO_9595 and tr_A0A2R9CRB8_A0A2R9CRB8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8K066_A0A2J8K066_PANTR_9598 and tr_A0A2R9BJC0_A0A2R9BJC0_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6TR62_F6TR62_MACMU_9544 and tr_G7P780_G7P780_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6TR62_F6TR62_MACMU_9544 and tr_A0A2K6E2W1_A0A2K6E2W1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WIY2_F6WIY2_MACMU_9544 and tr_G7PAW1_G7PAW1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WIY2_F6WIY2_MACMU_9544 and tr_A0A2I3M690_A0A2I3M690_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WIY2_F6WIY2_MACMU_9544 and tr_A0A2K5LWE5_A0A2K5LWE5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WIY2_F6WIY2_MACMU_9544 and tr_A0A2K6DTH7_A0A2K6DTH7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WIY2_F6WIY2_MACMU_9544 and tr_A0A2K5Z3D4_A0A2K5Z3D4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GRY4_F7GRY4_MACMU_9544 and tr_A0A096MTP0_A0A096MTP0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GRY4_F7GRY4_MACMU_9544 and tr_A0A0D9RA86_A0A0D9RA86_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H0Z1R8_H0Z1R8_TAEGU_59729 and tr_A0A091F0A8_A0A091F0A8_CORBR_85066 are exactly identical! WARNING: Sequences tr_G7P4A1_G7P4A1_MACFA_9541 and tr_A0A2K5M1G2_A0A2K5M1G2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7P4A1_G7P4A1_MACFA_9541 and tr_A0A2K6DBR9_A0A2K6DBR9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3N626_A0A2I3N626_PAPAN_9555 and tr_A0A2K6DL83_A0A2K6DL83_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151NCW9_A0A151NCW9_ALLMI_8496 and tr_A0A1U8D4L9_A0A1U8D4L9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091EXV3_A0A091EXV3_CORBR_85066 and tr_A0A091J4M5_A0A091J4M5_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091ITR7_A0A091ITR7_EGRGA_188379 and tr_A0A091FMM0_A0A091FMM0_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091UMW2_A0A091UMW2_NIPNI_128390 and tr_A0A091FMM1_A0A091FMM1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091UMW2_A0A091UMW2_NIPNI_128390 and tr_A0A093I9N7_A0A093I9N7_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091UNY2_A0A091UNY2_NIPNI_128390 and tr_A0A087R6T5_A0A087R6T5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UNY2_A0A091UNY2_NIPNI_128390 and tr_A0A0A0AV56_A0A0A0AV56_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091W3S2_A0A091W3S2_NIPNI_128390 and tr_A0A091IIV1_A0A091IIV1_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A087QKL2_A0A087QKL2_APTFO_9233 and tr_A0A0A0AGW3_A0A0A0AGW3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0MGL2_A0A2I0MGL2_COLLI_8932 and tr_A0A1V4K5Z9_A0A1V4K5Z9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CKR8_A0A0V1CKR8_TRIBR_45882 and tr_A0A0V0V8P6_A0A0V0V8P6_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A1I7TWA8_A0A1I7TWA8_9PELO_1561998 and tr_A0A1I7TWA9_A0A1I7TWA9_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2D0PYK9_A0A2D0PYK9_ICTPU_7998 and tr_A0A2D0PZY1_A0A2D0PZY1_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 38 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/P27918/4_raxmlng_ancestral/P27918.raxml.reduced.phy Alignment comprises 1 partitions and 469 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 469 Gaps: 25.24 % Invariant sites: 0.21 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P27918/4_raxmlng_ancestral/P27918.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/P27918/3_mltree/P27918.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 118 / 9440 [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: -206299.873772 [00:00:00 -206299.873772] Initial branch length optimization [00:00:01 -204855.496567] Model parameter optimization (eps = 0.100000) [00:00:44] Tree #1, final logLikelihood: -204159.873123 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.109823,0.114087) (0.116211,1.212167) (0.394518,0.790516) (0.379448,1.409233) 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/P27918/4_raxmlng_ancestral/P27918.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P27918/4_raxmlng_ancestral/P27918.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P27918/4_raxmlng_ancestral/P27918.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P27918/4_raxmlng_ancestral/P27918.raxml.log Analysis started: 04-Jun-2021 13:39:37 / finished: 04-Jun-2021 13:40:26 Elapsed time: 49.005 seconds