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 02:23:44 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NP85/2_msa/Q9NP85_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NP85/3_mltree/Q9NP85.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NP85/4_raxmlng_ancestral/Q9NP85 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676224 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/Q9NP85/2_msa/Q9NP85_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 383 sites WARNING: Sequences tr_B4QR04_B4QR04_DROSI_7240 and tr_B4HU85_B4HU85_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4R7B4_B4R7B4_DROSI_7240 and tr_B4I718_B4I718_DROSE_7238 are exactly identical! WARNING: Sequences tr_J3KBJ4_J3KBJ4_COCIM_246410 and tr_A0A0J6YKT9_A0A0J6YKT9_COCIT_404692 are exactly identical! WARNING: Sequences tr_G3RH62_G3RH62_GORGO_9595 and tr_H2Q0P5_H2Q0P5_PANTR_9598 are exactly identical! WARNING: Sequences tr_B5DNA4_B5DNA4_DROPS_46245 and tr_B4GVF8_B4GVF8_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A179UF62_A0A179UF62_BLAGS_559298 and tr_C5G8Y1_C5G8Y1_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A2I3T2A1_A0A2I3T2A1_PANTR_9598 and sp_P27105_STOM_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3T2A1_A0A2I3T2A1_PANTR_9598 and tr_A0A2R9AUH5_A0A2R9AUH5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q7G0_H2Q7G0_PANTR_9598 and sp_Q8TAV4_STML3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q7G0_H2Q7G0_PANTR_9598 and tr_A0A2R9BA49_A0A2R9BA49_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0K0JG65_A0A0K0JG65_BRUMA_6279 and tr_A0A044SU50_A0A044SU50_ONCVO_6282 are exactly identical! WARNING: Sequences tr_A2QE43_A2QE43_ASPNC_425011 and tr_G3Y0W6_G3Y0W6_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QE43_A2QE43_ASPNC_425011 and tr_A0A319AQF7_A0A319AQF7_9EURO_1450533 are exactly identical! WARNING: Sequences tr_E5S5N2_E5S5N2_TRISP_6334 and tr_A0A0V0RQW5_A0A0V0RQW5_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5S5N2_E5S5N2_TRISP_6334 and tr_A0A0V1DFH9_A0A0V1DFH9_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5S5N2_E5S5N2_TRISP_6334 and tr_A0A0V0WK77_A0A0V0WK77_9BILA_92179 are exactly identical! WARNING: Sequences tr_E5S5N2_E5S5N2_TRISP_6334 and tr_A0A0V0V0F9_A0A0V0V0F9_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5S5N2_E5S5N2_TRISP_6334 and tr_A0A0V1LSJ6_A0A0V1LSJ6_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5S5N2_E5S5N2_TRISP_6334 and tr_A0A0V1A325_A0A0V1A325_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5S5N2_E5S5N2_TRISP_6334 and tr_A0A0V1PGL0_A0A0V1PGL0_9BILA_92180 are exactly identical! WARNING: Sequences tr_G0N7P5_G0N7P5_CAEBE_135651 and tr_A0A1I7T8U4_A0A1I7T8U4_9PELO_1561998 are exactly identical! WARNING: Sequences tr_E3MA17_E3MA17_CAERE_31234 and tr_A0A261CIE3_A0A261CIE3_9PELO_1503980 are exactly identical! WARNING: Sequences tr_E3MAP2_E3MAP2_CAERE_31234 and tr_A0A261CLS4_A0A261CLS4_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A8X5Q3_A8X5Q3_CAEBR_6238 and tr_A0A2G5SJ24_A0A2G5SJ24_9PELO_1611254 are exactly identical! WARNING: Sequences tr_A8XKQ8_A8XKQ8_CAEBR_6238 and tr_A0A2G5STT3_A0A2G5STT3_9PELO_1611254 are exactly identical! WARNING: Sequences tr_B3RKW0_B3RKW0_TRIAD_10228 and tr_A0A369RW28_A0A369RW28_9METZ_287889 are exactly identical! WARNING: Sequences tr_G7P931_G7P931_MACFA_9541 and tr_A0A2I3M6J1_A0A2I3M6J1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7P931_G7P931_MACFA_9541 and tr_A0A0D9RNN7_A0A0D9RNN7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7P931_G7P931_MACFA_9541 and tr_A0A2K6BB43_A0A2K6BB43_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A015L7L3_A0A015L7L3_9GLOM_1432141 and tr_A0A2H5SRP3_A0A2H5SRP3_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015LSM6_A0A015LSM6_9GLOM_1432141 and tr_A0A2H5T7U6_A0A2H5T7U6_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A096P0P4_A0A096P0P4_PAPAN_9555 and tr_A0A0D9RLJ0_A0A0D9RLJ0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P0P4_A0A096P0P4_PAPAN_9555 and tr_A0A2K5KSA9_A0A2K5KSA9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P0P4_A0A096P0P4_PAPAN_9555 and tr_A0A2K5XVN7_A0A2K5XVN7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9RIC4_A0A0D9RIC4_CHLSB_60711 and tr_A0A2K5MPC1_A0A2K5MPC1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0K0FK47_A0A0K0FK47_STRVS_75913 and tr_A0A0K0EHR6_A0A0K0EHR6_STRER_6248 are exactly identical! WARNING: Sequences tr_A0A0K0FK47_A0A0K0FK47_STRVS_75913 and tr_A0A090L1B6_A0A090L1B6_STRRB_34506 are exactly identical! WARNING: Sequences tr_A0A0A1NUI9_A0A0A1NUI9_9FUNG_58291 and tr_A0A367J2T2_A0A367J2T2_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0V0RUG9_A0A0V0RUG9_9BILA_6336 and tr_A0A0V1CXT0_A0A0V1CXT0_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RUG9_A0A0V0RUG9_9BILA_6336 and tr_A0A0V0X8C6_A0A0V0X8C6_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RUG9_A0A0V0RUG9_9BILA_6336 and tr_A0A0V0ZWX2_A0A0V0ZWX2_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RUG9_A0A0V0RUG9_9BILA_6336 and tr_A0A0V1K430_A0A0V1K430_TRIPS_6337 are exactly identical! WARNING: Sequences tr_A0A0V0RUG9_A0A0V0RUG9_9BILA_6336 and tr_A0A0V1PEA1_A0A0V1PEA1_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RUG9_A0A0V0RUG9_9BILA_6336 and tr_A0A0V0U551_A0A0V0U551_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A100IA18_A0A100IA18_ASPNG_5061 and tr_A0A1L9N7Y9_A0A1L9N7Y9_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A1L9X960_A0A1L9X960_ASPAC_690307 and tr_A0A2V5IRI9_A0A2V5IRI9_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A1L9X960_A0A1L9X960_ASPAC_690307 and tr_A0A2V5HA65_A0A2V5HA65_9EURO_1450538 are exactly identical! WARNING: Sequences tr_A0A1Y1WPZ7_A0A1Y1WPZ7_9FUNG_1314790 and tr_A0A1Y1XTD8_A0A1Y1XTD8_9FUNG_1314790 are exactly identical! WARNING: Sequences tr_A0A2G4SQM0_A0A2G4SQM0_9FUNG_1340429 and tr_A0A367J1A4_A0A367J1A4_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A2U4CHW8_A0A2U4CHW8_TURTR_9739 and tr_A0A2U4CHX5_A0A2U4CHX5_TURTR_9739 are exactly identical! WARNING: Duplicate sequences found: 50 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/Q9NP85/4_raxmlng_ancestral/Q9NP85.raxml.reduced.phy Alignment comprises 1 partitions and 383 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 383 Gaps: 28.38 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NP85/4_raxmlng_ancestral/Q9NP85.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/Q9NP85/3_mltree/Q9NP85.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 96 / 7680 [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: -147082.172936 [00:00:00 -147082.172936] Initial branch length optimization [00:00:01 -143663.550525] Model parameter optimization (eps = 0.100000) [00:00:46] Tree #1, final logLikelihood: -142072.086770 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.279939,0.313318) (0.150161,0.656970) (0.263403,0.560794) (0.306497,2.172691) 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/Q9NP85/4_raxmlng_ancestral/Q9NP85.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NP85/4_raxmlng_ancestral/Q9NP85.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NP85/4_raxmlng_ancestral/Q9NP85.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NP85/4_raxmlng_ancestral/Q9NP85.raxml.log Analysis started: 03-Jun-2021 02:23:44 / finished: 03-Jun-2021 02:24:34 Elapsed time: 49.856 seconds Consumed energy: 4.073 Wh