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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 03-Jun-2021 02:01:42 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48029/2_msa/P48029_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48029/3_mltree/P48029.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48029/4_raxmlng_ancestral/P48029 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674902 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/P48029/2_msa/P48029_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 635 sites WARNING: Sequences tr_B4QI04_B4QI04_DROSI_7240 and sp_Q7K4Y6_DAT_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QI04_B4QI04_DROSI_7240 and tr_B4HSZ4_B4HSZ4_DROSE_7238 are exactly identical! WARNING: Sequences sp_P31648_SC6A1_MOUSE_10090 and sp_P23978_SC6A1_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Z0E9_M3Z0E9_MUSPF_9669 and tr_E2RKV9_E2RKV9_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z0E9_M3Z0E9_MUSPF_9669 and tr_A0A2I2UPJ1_A0A2I2UPJ1_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z0E9_M3Z0E9_MUSPF_9669 and tr_A0A2U3YMF9_A0A2U3YMF9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z0N5_M3Z0N5_MUSPF_9669 and tr_A0A2Y9J8H8_A0A2Y9J8H8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3FZC9_A0A2I3FZC9_NOMLE_61853 and tr_G3RC38_G3RC38_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3FZC9_A0A2I3FZC9_NOMLE_61853 and tr_A0A2I3SWR4_A0A2I3SWR4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_H2PA22_H2PA22_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_H2QM23_H2QM23_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and sp_P30531_SC6A1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_F6WVM8_F6WVM8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_G7NYT4_G7NYT4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A096NQ20_A0A096NQ20_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A0D9RC09_A0A0D9RC09_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2K6A0C9_A0A2K6A0C9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2R9CH47_A0A2R9CH47_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8MWT0_A0A2J8MWT0_PANTR_9598 and tr_A0A2R9AJ86_A0A2R9AJ86_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7DP91_K7DP91_PANTR_9598 and sp_P48029_SC6A8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6Z3A6_F6Z3A6_HORSE_9796 and tr_A0A1U7TXN5_A0A1U7TXN5_TARSY_1868482 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_G7PIL7_G7PIL7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_A0A096NC41_A0A096NC41_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_A0A0D9RAK2_A0A0D9RAK2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_A0A2K5L7Z6_A0A2K5L7Z6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_A0A2K6DHL4_A0A2K6DHL4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_A0A2K5ZYU9_A0A2K5ZYU9_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0ZQY1_H0ZQY1_TAEGU_59729 and tr_A0A218V974_A0A218V974_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3KDU8_U3KDU8_FICAL_59894 and tr_A0A091ENZ6_A0A091ENZ6_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3KDU8_U3KDU8_FICAL_59894 and tr_A0A091VHN5_A0A091VHN5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3KDU8_U3KDU8_FICAL_59894 and tr_A0A093G6B4_A0A093G6B4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_U3KDU8_U3KDU8_FICAL_59894 and tr_A0A091I6F5_A0A091I6F5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A096MYM4_A0A096MYM4_PAPAN_9555 and tr_A0A2K5LFH9_A0A2K5LFH9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N2F3_A0A096N2F3_PAPAN_9555 and tr_A0A2K6BWY5_A0A2K6BWY5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151MK13_A0A151MK13_ALLMI_8496 and tr_A0A1U8CTU6_A0A1U8CTU6_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NFM2_A0A151NFM2_ALLMI_8496 and tr_A0A1U7S8D9_A0A1U7S8D9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NIH4_A0A151NIH4_ALLMI_8496 and tr_A0A1U7SBY4_A0A1U7SBY4_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151PBK1_A0A151PBK1_ALLMI_8496 and tr_A0A1U7SB16_A0A1U7SB16_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091VSV1_A0A091VSV1_NIPNI_128390 and tr_A0A087RH38_A0A087RH38_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VSV1_A0A091VSV1_NIPNI_128390 and tr_A0A091WBW6_A0A091WBW6_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091VSV1_A0A091VSV1_NIPNI_128390 and tr_A0A0A0ATB2_A0A0A0ATB2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091W8F8_A0A091W8F8_OPIHO_30419 and tr_A0A218VCV3_A0A218VCV3_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2I0LVM4_A0A2I0LVM4_COLLI_8932 and tr_A0A1V4JII7_A0A1V4JII7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CJ51_A0A0V1CJ51_TRIBR_45882 and tr_A0A0V0VPP5_A0A0V0VPP5_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CJ51_A0A0V1CJ51_TRIBR_45882 and tr_A0A0V0ZD68_A0A0V0ZD68_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CJ51_A0A0V1CJ51_TRIBR_45882 and tr_A0A0V1MYG8_A0A0V1MYG8_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V1L239_A0A0V1L239_9BILA_6335 and tr_A0A0V1NLY7_A0A0V1NLY7_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A226MXQ4_A0A226MXQ4_CALSU_9009 and tr_A0A226PLR4_A0A226PLR4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NG47_A0A226NG47_CALSU_9009 and tr_A0A226PF47_A0A226PF47_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RWR4_A0A2D0RWR4_ICTPU_7998 and tr_A0A2D0RYA2_A0A2D0RYA2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KJE1_A0A2K5KJE1_CERAT_9531 and tr_A0A2K6APW9_A0A2K6APW9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5KZH8_A0A2K5KZH8_CERAT_9531 and tr_A0A2K6BVQ8_A0A2K6BVQ8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K6AA20_A0A2K6AA20_MANLE_9568 and tr_A0A2R9B9J4_A0A2R9B9J4_PANPA_9597 are exactly identical! WARNING: Duplicate sequences found: 53 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/P48029/4_raxmlng_ancestral/P48029.raxml.reduced.phy Alignment comprises 1 partitions and 635 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 635 Gaps: 12.34 % Invariant sites: 0.16 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48029/4_raxmlng_ancestral/P48029.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/P48029/3_mltree/P48029.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 159 / 12720 [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: -209329.211673 [00:00:00 -209329.211673] Initial branch length optimization [00:00:02 -208989.512844] Model parameter optimization (eps = 0.100000) [00:00:53] Tree #1, final logLikelihood: -208038.353836 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.247712,0.349163) (0.337635,0.476362) (0.252432,1.227633) (0.162221,2.729472) 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/P48029/4_raxmlng_ancestral/P48029.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48029/4_raxmlng_ancestral/P48029.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48029/4_raxmlng_ancestral/P48029.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48029/4_raxmlng_ancestral/P48029.raxml.log Analysis started: 03-Jun-2021 02:01:42 / finished: 03-Jun-2021 02:02:42 Elapsed time: 60.057 seconds Consumed energy: 3.516 Wh