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 19-Jul-2021 13:41:54 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75489/2_msa/O75489_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75489/3_mltree/O75489.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75489/4_raxmlng_ancestral/O75489 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626691314 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_300621/phylogeny-snakemake/results/O75489/2_msa/O75489_nogap_msa.fasta [00:00:00] Loaded alignment with 898 taxa and 264 sites WARNING: Sequences tr_B4QP26_B4QP26_DROSI_7240 and tr_B4HTK8_B4HTK8_DROSE_7238 are exactly identical! WARNING: Sequences tr_J3KJ14_J3KJ14_COCIM_246410 and tr_E9CWJ1_E9CWJ1_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KJ14_J3KJ14_COCIM_246410 and tr_A0A0J6Y3U1_A0A0J6Y3U1_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QB05_B6QB05_TALMQ_441960 and tr_A0A093VBW4_A0A093VBW4_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2VWB3_B2VWB3_PYRTR_426418 and tr_A0A2W1EIS6_A0A2W1EIS6_9PLEO_45151 are exactly identical! WARNING: Sequences tr_C0NRX0_C0NRX0_AJECG_447093 and tr_C6HD64_C6HD64_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NRX0_C0NRX0_AJECG_447093 and tr_F0UTY5_F0UTY5_AJEC8_544711 are exactly identical! WARNING: Sequences sp_P23710_NDUS3_NEUCR_367110 and tr_G4UZ54_G4UZ54_NEUT9_510952 are exactly identical! WARNING: Sequences tr_A0A179UCP0_A0A179UCP0_BLAGS_559298 and tr_C5GGX3_C5GGX3_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2Q3J2_H2Q3J2_PANTR_9598 and tr_A0A2R9AFM3_A0A2R9AFM3_PANPA_9597 are exactly identical! WARNING: Sequences tr_E9ENX7_E9ENX7_METRA_655844 and tr_A0A0B4IBI7_A0A0B4IBI7_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9ENX7_E9ENX7_METRA_655844 and tr_A0A0D9P6N3_A0A0D9P6N3_METAN_1291518 are exactly identical! WARNING: Sequences tr_J4UQW0_J4UQW0_BEAB2_655819 and tr_A0A0A2VPP4_A0A0A2VPP4_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J4UQW0_J4UQW0_BEAB2_655819 and tr_A0A2N6NXD4_A0A2N6NXD4_BEABA_176275 are exactly identical! WARNING: Sequences tr_K3Z2I1_K3Z2I1_SETIT_4555 and tr_M0Z344_M0Z344_HORVV_112509 are exactly identical! WARNING: Sequences tr_K3Z2I1_K3Z2I1_SETIT_4555 and tr_A0A2T7C756_A0A2T7C756_9POAL_1504633 are exactly identical! WARNING: Sequences tr_Q2UN03_Q2UN03_ASPOR_510516 and tr_A0A1S9D6F5_A0A1S9D6F5_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_G7X9Y8_G7X9Y8_ASPKW_1033177 and tr_A0A146F8H9_A0A146F8H9_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G2YSG5_G2YSG5_BOTF4_999810 and tr_M7UCS0_M7UCS0_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SDW6_F2SDW6_TRIRC_559305 and tr_A0A178EV14_A0A178EV14_TRIRU_5551 are exactly identical! WARNING: Sequences tr_D4B0J6_D4B0J6_ARTBC_663331 and tr_A0A059J073_A0A059J073_9EURO_1215338 are exactly identical! WARNING: Sequences tr_B3RJ43_B3RJ43_TRIAD_10228 and tr_A0A369SL27_A0A369SL27_9METZ_287889 are exactly identical! WARNING: Sequences tr_G3YD64_G3YD64_ASPNA_380704 and tr_A0A319AWR8_A0A319AWR8_9EURO_1450533 are exactly identical! WARNING: Sequences tr_L2G1V5_L2G1V5_COLFN_1213859 and tr_T0M3F9_T0M3F9_COLGC_1237896 are exactly identical! WARNING: Sequences tr_S0DQ69_S0DQ69_GIBF5_1279085 and tr_A0A365NDG4_A0A365NDG4_GIBIN_948311 are exactly identical! WARNING: Sequences tr_V2XXH7_V2XXH7_MONRO_1381753 and tr_A0A0W0FXY5_A0A0W0FXY5_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A010QPH7_A0A010QPH7_9PEZI_1445577 and tr_A0A1G4AYQ6_A0A1G4AYQ6_9PEZI_1209926 are exactly identical! WARNING: Sequences tr_A0A015MSX5_A0A015MSX5_9GLOM_1432141 and tr_A0A2I1EQR9_A0A2I1EQR9_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A2K6VJN9_A0A2K6VJN9_ONCVO_6282 and tr_A0A182EEQ1_A0A182EEQ1_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A084QVD4_A0A084QVD4_STAC4_1283841 and tr_A0A084RF98_A0A084RF98_STACH_1283842 are exactly identical! WARNING: Sequences tr_A0A0A1MMF8_A0A0A1MMF8_9FUNG_58291 and tr_A0A0A1PJJ0_A0A0A1PJJ0_9FUNG_58291 are exactly identical! WARNING: Sequences tr_A0A0F7VHS0_A0A0F7VHS0_9EURO_104259 and tr_A0A1Q5TD84_A0A1Q5TD84_9EURO_1316194 are exactly identical! WARNING: Sequences tr_A0A0S7DG01_A0A0S7DG01_9EURO_293939 and tr_A0A2I1CD02_A0A2I1CD02_9EURO_1392255 are exactly identical! WARNING: Sequences tr_A0A117E0D6_A0A117E0D6_ASPNG_5061 and tr_A0A1L9N1E6_A0A1L9N1E6_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A117E0D6_A0A117E0D6_ASPNG_5061 and tr_A0A317W7E8_A0A317W7E8_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A0E0SAR4_A0A0E0SAR4_GIBZE_229533 and tr_A0A2T4GCS9_A0A2T4GCS9_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A164UIF6_A0A164UIF6_9HOMO_1314777 and tr_A0A166IPC6_A0A166IPC6_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A0M4JB57_A0A0M4JB57_TOBAC_4097 and tr_A0A075W230_A0A075W230_CAPAN_4072 are exactly identical! WARNING: Sequences tr_B5XG99_B5XG99_SALSA_8030 and tr_A0A060VXX8_A0A060VXX8_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1B8E655_A0A1B8E655_9PEZI_1524831 and tr_A0A1B8GVR9_A0A1B8GVR9_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A1B8E655_A0A1B8E655_9PEZI_1524831 and tr_A0A1B8CQ55_A0A1B8CQ55_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A1B8AH27_A0A1B8AH27_FUSPO_36050 and tr_A0A2L2TKD4_A0A2L2TKD4_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A1B7NIS1_A0A1B7NIS1_9HOMO_1314800 and tr_A0A1J8QZG9_A0A1J8QZG9_9HOMO_180088 are exactly identical! WARNING: Sequences tr_A0A226MYK1_A0A226MYK1_CALSU_9009 and tr_A0A226PS25_A0A226PS25_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3TA74_A0A2H3TA74_FUSOX_5507 and tr_A0A2H3HN89_A0A2H3HN89_FUSOX_327505 are exactly identical! WARNING: Sequences tr_A0A319BY60_A0A319BY60_9EURO_1448315 and tr_A0A2V5IMH3_A0A2V5IMH3_9EURO_1450541 are exactly identical! WARNING: Duplicate sequences found: 46 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75489/4_raxmlng_ancestral/O75489.raxml.reduced.phy Alignment comprises 1 partitions and 264 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 264 Gaps: 15.71 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75489/4_raxmlng_ancestral/O75489.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_300621/phylogeny-snakemake/results/O75489/3_mltree/O75489.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 66 / 5280 [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: -91280.400642 [00:00:00 -91280.400642] Initial branch length optimization [00:00:00 -85215.736804] Model parameter optimization (eps = 0.100000) [00:00:25] Tree #1, final logLikelihood: -84770.403599 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.178729,0.295576) (0.323991,0.466212) (0.233997,0.704769) (0.263283,2.397457) 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_300621/phylogeny-snakemake/results/O75489/4_raxmlng_ancestral/O75489.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75489/4_raxmlng_ancestral/O75489.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75489/4_raxmlng_ancestral/O75489.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O75489/4_raxmlng_ancestral/O75489.raxml.log Analysis started: 19-Jul-2021 13:41:54 / finished: 19-Jul-2021 13:42:21 Elapsed time: 27.587 seconds