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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 03-Jun-2021 02:33:27 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04637/2_msa/P04637_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04637/3_mltree/P04637.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04637/4_raxmlng_ancestral/P04637 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676807 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04637/2_msa/P04637_nogap_msa.fasta [00:00:00] Loaded alignment with 372 taxa and 393 sites WARNING: Sequences tr_A0A167VDT2_A0A167VDT2_CHICK_9031 and tr_G1MS14_G1MS14_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A2I3GNV1_A0A2I3GNV1_NOMLE_61853 and tr_A0A2I2Z434_A0A2I2Z434_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GNV1_A0A2I3GNV1_NOMLE_61853 and tr_H2QNY5_H2QNY5_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GNV1_A0A2I3GNV1_NOMLE_61853 and sp_Q9H3D4_P63_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GNV1_A0A2I3GNV1_NOMLE_61853 and tr_F7FN64_F7FN64_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GNV1_A0A2I3GNV1_NOMLE_61853 and tr_A0A2R8P0K0_A0A2R8P0K0_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3GNV1_A0A2I3GNV1_NOMLE_61853 and tr_G7NYP4_G7NYP4_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3GNV1_A0A2I3GNV1_NOMLE_61853 and tr_A0A2I3MNM6_A0A2I3MNM6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GNV1_A0A2I3GNV1_NOMLE_61853 and tr_A0A2K5MIG1_A0A2K5MIG1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GNV1_A0A2I3GNV1_NOMLE_61853 and tr_A0A2K6BU74_A0A2K6BU74_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GNV1_A0A2I3GNV1_NOMLE_61853 and tr_A0A2R9BLB5_A0A2R9BLB5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1PSQ3_G1PSQ3_MYOLU_59463 and tr_F7B2P6_F7B2P6_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1PSQ3_G1PSQ3_MYOLU_59463 and tr_W5QGZ8_W5QGZ8_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1PSQ3_G1PSQ3_MYOLU_59463 and tr_I3MLP5_I3MLP5_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1PSQ3_G1PSQ3_MYOLU_59463 and tr_I3LPD4_I3LPD4_PIG_9823 are exactly identical! WARNING: Sequences tr_G1PSQ3_G1PSQ3_MYOLU_59463 and tr_F1MKA9_F1MKA9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1PSQ3_G1PSQ3_MYOLU_59463 and tr_A0A2Y9N7Z3_A0A2Y9N7Z3_DELLE_9749 are exactly identical! WARNING: Sequences tr_G3GT84_G3GT84_CRIGR_10029 and tr_A0A3Q0CT16_A0A3Q0CT16_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I3RJD2_A0A2I3RJD2_PANTR_9598 and sp_O15350_P73_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QC53_H2QC53_PANTR_9598 and sp_P04637_P53_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QC53_H2QC53_PANTR_9598 and tr_A0A2R9A5P4_A0A2R9A5P4_PANPA_9597 are exactly identical! WARNING: Sequences sp_P56424_P53_MACMU_9544 and tr_G7PTI9_G7PTI9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3TYZ8_G3TYZ8_LOXAF_9785 and tr_A0A2Y9DWD9_A0A2Y9DWD9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G3TYZ8_G3TYZ8_LOXAF_9785 and tr_A0A384B7M4_A0A384B7M4_BALAS_310752 are exactly identical! WARNING: Sequences tr_G1L1S8_G1L1S8_AILME_9646 and tr_A0A2I2U634_A0A2I2U634_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1L1S8_G1L1S8_AILME_9646 and tr_A0A384D9C8_A0A384D9C8_URSMA_29073 are exactly identical! WARNING: Sequences tr_U3JY64_U3JY64_FICAL_59894 and tr_A0A091EA06_A0A091EA06_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A151MM54_A0A151MM54_ALLMI_8496 and tr_A0A3Q0GFS3_A0A3Q0GFS3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091VBV4_A0A091VBV4_NIPNI_128390 and tr_A0A087R7Z2_A0A087R7Z2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A099ZPQ3_A0A099ZPQ3_TINGU_94827 and tr_A0A093GLW0_A0A093GLW0_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A1S3RGF1_A0A1S3RGF1_SALSA_8030 and tr_C0H8X1_C0H8X1_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A2K5N3Z0_A0A2K5N3Z0_CERAT_9531 and tr_A0A2K6AAI9_A0A2K6AAI9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3V4Q3_A0A2U3V4Q3_TURTR_9739 and tr_A0A2Y9EHW3_A0A2Y9EHW3_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 33 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04637/4_raxmlng_ancestral/P04637.raxml.reduced.phy Alignment comprises 1 partitions and 393 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 393 Gaps: 16.85 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04637/4_raxmlng_ancestral/P04637.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04637/3_mltree/P04637.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 99 / 7920 [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: -70034.259321 [00:00:00 -70034.259321] Initial branch length optimization [00:00:00 -65833.321037] Model parameter optimization (eps = 0.100000) [00:00:17] Tree #1, final logLikelihood: -65613.601700 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.177154,0.376964) (0.110532,0.474369) (0.346570,0.753922) (0.365744,1.693806) 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04637/4_raxmlng_ancestral/P04637.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04637/4_raxmlng_ancestral/P04637.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04637/4_raxmlng_ancestral/P04637.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04637/4_raxmlng_ancestral/P04637.raxml.log Analysis started: 03-Jun-2021 02:33:27 / finished: 03-Jun-2021 02:33:46 Elapsed time: 18.700 seconds Consumed energy: 1.643 Wh