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 17-Jun-2021 23:59:22 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29597/2_msa/P29597_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29597/3_mltree/P29597.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29597/4_raxmlng_ancestral/P29597 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1623963562 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/P29597/2_msa/P29597_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1187 sites WARNING: Sequences sp_Q61527_ERBB4_MOUSE_10090 and tr_A0A1U7QBV4_A0A1U7QBV4_MESAU_10036 are exactly identical! WARNING: Sequences tr_G9K914_G9K914_MUSPF_9669 and tr_A0A2Y9KDK4_A0A2Y9KDK4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3R096_G3R096_GORGO_9595 and tr_A0A2I3TMU8_A0A2I3TMU8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R9U2_G3R9U2_GORGO_9595 and tr_H2PQC0_H2PQC0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R9U2_G3R9U2_GORGO_9595 and tr_H2R453_H2R453_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R9U2_G3R9U2_GORGO_9595 and sp_P07948_LYN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_A0A2J8MRU2_A0A2J8MRU2_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and sp_Q16620_NTRK2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_F7DGW1_F7DGW1_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_G7PSM1_G7PSM1_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_A0A2I3MH64_A0A2I3MH64_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_A0A2K5NCA1_A0A2K5NCA1_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_A0A2K6BIB6_A0A2K6BIB6_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_A0A2R9BIL6_A0A2R9BIL6_PANPA_9597 are exactly identical! WARNING: Sequences tr_E2RKA1_E2RKA1_CANLF_9615 and tr_G1LBG1_G1LBG1_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2I3SYV7_A0A2I3SYV7_PANTR_9598 and tr_A0A2R8ZP32_A0A2R8ZP32_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0K0J668_A0A0K0J668_BRUMA_6279 and tr_A0A0R3QQM9_A0A0R3QQM9_9BILA_42155 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 tr_F7BV42_F7BV42_MACMU_9544 and tr_G7PBV3_G7PBV3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7BV42_F7BV42_MACMU_9544 and tr_A0A096MX07_A0A096MX07_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7BV42_F7BV42_MACMU_9544 and tr_A0A0D9RQ35_A0A0D9RQ35_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7BV42_F7BV42_MACMU_9544 and tr_A0A2K6DNJ8_A0A2K6DNJ8_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZLG0_H0ZLG0_TAEGU_59729 and tr_A0A218VBI1_A0A218VBI1_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3K8U1_U3K8U1_FICAL_59894 and tr_A0A218UB11_A0A218UB11_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2I0M6K5_A0A2I0M6K5_COLLI_8932 and tr_A0A1V4JCZ7_A0A1V4JCZ7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CPJ3_A0A0V1CPJ3_TRIBR_45882 and tr_A0A0V0UXY2_A0A0V0UXY2_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CPJ3_A0A0V1CPJ3_TRIBR_45882 and tr_A0A0V1A3N2_A0A0V1A3N2_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A226NGR7_A0A226NGR7_CALSU_9009 and tr_A0A226NY66_A0A226NY66_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0SR82_A0A2D0SR82_ICTPU_7998 and tr_A0A2D0SSC0_A0A2D0SSC0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T7Y0_A0A2D0T7Y0_ICTPU_7998 and tr_A0A2D0T8L0_A0A2D0T8L0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4AJ04_A0A2U4AJ04_TURTR_9739 and tr_A0A2Y9LZZ2_A0A2Y9LZZ2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C7U7_A0A2U4C7U7_TURTR_9739 and tr_A0A384B469_A0A384B469_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 34 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/P29597/4_raxmlng_ancestral/P29597.raxml.reduced.phy Alignment comprises 1 partitions and 1187 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1187 Gaps: 42.41 % Invariant sites: 0.08 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29597/4_raxmlng_ancestral/P29597.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/P29597/3_mltree/P29597.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 297 / 23760 [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: -345782.867546 [00:00:00 -345782.867546] Initial branch length optimization [00:00:03 -323309.524443] Model parameter optimization (eps = 0.100000) [00:01:23] Tree #1, final logLikelihood: -322600.626068 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.124396,0.320213) (0.101961,0.401938) (0.410737,0.743102) (0.362905,1.691805) 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/P29597/4_raxmlng_ancestral/P29597.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29597/4_raxmlng_ancestral/P29597.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29597/4_raxmlng_ancestral/P29597.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29597/4_raxmlng_ancestral/P29597.raxml.log Analysis started: 17-Jun-2021 23:59:22 / finished: 18-Jun-2021 00:00:55 Elapsed time: 92.878 seconds Consumed energy: 7.391 Wh