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 13:35:27 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O94804/2_msa/O94804_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O94804/3_mltree/O94804.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O94804/4_raxmlng_ancestral/O94804 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802927 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/O94804/2_msa/O94804_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 968 sites WARNING: Sequences sp_Q9Z2W1_STK25_MOUSE_10090 and tr_Q6V9V9_Q6V9V9_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Z1S0_M3Z1S0_MUSPF_9669 and tr_A0A2Y9INI5_A0A2Y9INI5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_A0A2J8UF55_A0A2J8UF55_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_F6URD2_F6URD2_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_A0A2I3SVA8_A0A2I3SVA8_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_G7PCA9_G7PCA9_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_A0JN96_A0JN96_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_A0A0D9RIR7_A0A0D9RIR7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_A0A2K5L7J1_A0A2K5L7J1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_A0A2K6B7S5_A0A2K6B7S5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_A0A2K5XZ51_A0A2K5XZ51_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_A0A2U4AIA2_A0A2U4AIA2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_A0A2U3XFR8_A0A2U3XFR8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_A0A2Y9PD37_A0A2Y9PD37_DELLE_9749 are exactly identical! WARNING: Sequences tr_J3K3K4_J3K3K4_COCIM_246410 and tr_A0A0J6YDX7_A0A0J6YDX7_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6Q8M4_B6Q8M4_TALMQ_441960 and tr_A0A093VC69_A0A093VC69_TALMA_1077442 are exactly identical! WARNING: Sequences tr_A0A2I2ZHZ0_A0A2I2ZHZ0_GORGO_9595 and tr_G1L109_G1L109_AILME_9646 are exactly identical! WARNING: Sequences tr_H2NL78_H2NL78_PONAB_9601 and tr_H2Q8A0_H2Q8A0_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NL78_H2NL78_PONAB_9601 and sp_Q9Y4K4_M4K5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NL78_H2NL78_PONAB_9601 and tr_A0A2R8ZNS2_A0A2R8ZNS2_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q290P0_Q290P0_DROPS_46245 and tr_B4GBG4_B4GBG4_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8MW16_B8MW16_ASPFN_332952 and tr_Q2UT83_Q2UT83_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8MW16_B8MW16_ASPFN_332952 and tr_A0A1S9DWU0_A0A1S9DWU0_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UZW1_A0A179UZW1_BLAGS_559298 and tr_C5GQY8_C5GQY8_AJEDR_559297 are exactly identical! WARNING: Sequences tr_E2RGP4_E2RGP4_CANLF_9615 and tr_A0A2U3WH70_A0A2U3WH70_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3T3U0_A0A2I3T3U0_PANTR_9598 and tr_A0A2R8ZUF2_A0A2R8ZUF2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q2J3_H2Q2J3_PANTR_9598 and sp_Q9H2G2_SLK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q2J3_H2Q2J3_PANTR_9598 and tr_A0A2R9CSE7_A0A2R9CSE7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A2R1E1_A2R1E1_ASPNC_425011 and tr_A0A319B9L1_A0A319B9L1_9EURO_1450533 are exactly identical! WARNING: Sequences sp_A4K2T0_STK4_MACMU_9544 and tr_A0A096NX80_A0A096NX80_PAPAN_9555 are exactly identical! WARNING: Sequences sp_A4K2T0_STK4_MACMU_9544 and tr_A0A0D9RP63_A0A0D9RP63_CHLSB_60711 are exactly identical! WARNING: Sequences sp_A4K2T0_STK4_MACMU_9544 and tr_A0A2K5YCM9_A0A2K5YCM9_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7D279_F7D279_MACMU_9544 and tr_G7PA84_G7PA84_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7D279_F7D279_MACMU_9544 and tr_A0A096NUW8_A0A096NUW8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7D279_F7D279_MACMU_9544 and tr_A0A2K5N4A4_A0A2K5N4A4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7D279_F7D279_MACMU_9544 and tr_A0A2K6C1F6_A0A2K6C1F6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7D279_F7D279_MACMU_9544 and tr_A0A2K5YK04_A0A2K5YK04_MANLE_9568 are exactly identical! WARNING: Sequences tr_F4X6R2_F4X6R2_ACREC_103372 and tr_A0A195E7M5_A0A195E7M5_9HYME_471704 are exactly identical! WARNING: Sequences tr_G7PDW9_G7PDW9_MACFA_9541 and tr_A0A2K6C168_A0A2K6C168_MACNE_9545 are exactly identical! WARNING: Sequences sp_E1BK52_STK10_BOVIN_9913 and tr_H2XJF0_H2XJF0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2K6VYR1_A0A2K6VYR1_ONCVO_6282 and tr_A0A182EDH7_A0A182EDH7_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0D9QZ33_A0A0D9QZ33_CHLSB_60711 and tr_A0A2K5LRI3_A0A2K5LRI3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151MY95_A0A151MY95_ALLMI_8496 and tr_A0A091J6U2_A0A091J6U2_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A151MY95_A0A151MY95_ALLMI_8496 and tr_A0A093Q3P8_A0A093Q3P8_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A151MY95_A0A151MY95_ALLMI_8496 and tr_A0A093GFH4_A0A093GFH4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A151MY95_A0A151MY95_ALLMI_8496 and tr_A0A091J6Z5_A0A091J6Z5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0W8DNM9_A0A0W8DNM9_PHYNI_4790 and tr_W2K6Z3_W2K6Z3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0V0RVV3_A0A0V0RVV3_9BILA_6336 and tr_A0A0V1L179_A0A0V1L179_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A124BYX0_A0A124BYX0_ASPNG_5061 and tr_A0A1L9NE81_A0A1L9NE81_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A1S3XUR2_A0A1S3XUR2_TOBAC_4097 and tr_A0A1U7X252_A0A1U7X252_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2U4C223_A0A2U4C223_TURTR_9739 and tr_A0A2Y9PXE7_A0A2Y9PXE7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C223_A0A2U4C223_TURTR_9739 and tr_A0A2Y9T1A9_A0A2Y9T1A9_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 52 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/O94804/4_raxmlng_ancestral/O94804.raxml.reduced.phy Alignment comprises 1 partitions and 968 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 968 Gaps: 37.98 % Invariant sites: 0.41 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O94804/4_raxmlng_ancestral/O94804.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/O94804/3_mltree/O94804.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 242 / 19360 [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: -343407.474812 [00:00:00 -343407.474812] Initial branch length optimization [00:00:02 -302222.968026] Model parameter optimization (eps = 0.100000) [00:01:09] Tree #1, final logLikelihood: -301684.718594 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.120734,0.166016) (0.089409,0.226431) (0.400442,0.705431) (0.389414,1.739090) 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/O94804/4_raxmlng_ancestral/O94804.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O94804/4_raxmlng_ancestral/O94804.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O94804/4_raxmlng_ancestral/O94804.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O94804/4_raxmlng_ancestral/O94804.raxml.log Analysis started: 04-Jun-2021 13:35:27 / finished: 04-Jun-2021 13:36:45 Elapsed time: 78.011 seconds