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 01:54:14 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15056/2_msa/P15056_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15056/3_mltree/P15056.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15056/4_raxmlng_ancestral/P15056 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674454 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/P15056/2_msa/P15056_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 766 sites WARNING: Sequences tr_B4R3I0_B4R3I0_DROSI_7240 and sp_P11346_KRAF1_DROME_7227 are exactly identical! WARNING: Sequences tr_B4R3I0_B4R3I0_DROSI_7240 and tr_B4I9U9_B4I9U9_DROSE_7238 are exactly identical! WARNING: Sequences sp_P05625_RAF1_CHICK_9031 and tr_G1N0N1_G1N0N1_MELGA_9103 are exactly identical! WARNING: Sequences tr_G1QHI1_G1QHI1_NOMLE_61853 and tr_G3R2Q8_G3R2Q8_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QHI1_G1QHI1_NOMLE_61853 and tr_H2Q6Z2_H2Q6Z2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QHI1_G1QHI1_NOMLE_61853 and sp_Q6VAB6_KSR2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QHI1_G1QHI1_NOMLE_61853 and tr_A0A2I3MDP2_A0A2I3MDP2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QHI1_G1QHI1_NOMLE_61853 and tr_A0A2K6DZ55_A0A2K6DZ55_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QHI1_G1QHI1_NOMLE_61853 and tr_A0A2K6AET8_A0A2K6AET8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QHI1_G1QHI1_NOMLE_61853 and tr_A0A2R9AW42_A0A2R9AW42_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3ZCA6_M3ZCA6_NOMLE_61853 and sp_Q5R5M7_RAF1_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3ZCA6_M3ZCA6_NOMLE_61853 and sp_P04049_RAF1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3ZCA6_M3ZCA6_NOMLE_61853 and tr_A0A1D5R9U8_A0A1D5R9U8_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3ZCA6_M3ZCA6_NOMLE_61853 and tr_A0A2I3N2V3_A0A2I3N2V3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3ZCA6_M3ZCA6_NOMLE_61853 and tr_A0A2K5MHK5_A0A2K5MHK5_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3ZCA6_M3ZCA6_NOMLE_61853 and tr_A0A2K6DFM6_A0A2K6DFM6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R027_G3R027_GORGO_9595 and tr_K6ZK74_K6ZK74_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R027_G3R027_GORGO_9595 and sp_P10398_ARAF_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R027_G3R027_GORGO_9595 and tr_A0A2R8ZFY7_A0A2R8ZFY7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SB57_G3SB57_GORGO_9595 and tr_A0A2I3TK00_A0A2I3TK00_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SB57_G3SB57_GORGO_9595 and sp_P15056_BRAF_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SB57_G3SB57_GORGO_9595 and tr_A0A2R9BBV0_A0A2R9BBV0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3THL4_A0A2I3THL4_PANTR_9598 and tr_A0A2R9B7H5_A0A2R9B7H5_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5P071_W5P071_SHEEP_9940 and tr_F1RKG1_F1RKG1_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A088A6D1_A0A088A6D1_APIME_7460 and tr_A0A2A3E389_A0A2A3E389_APICC_94128 are exactly identical! WARNING: Sequences tr_H9FU32_H9FU32_MACMU_9544 and tr_A0A096MVH2_A0A096MVH2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9FU32_H9FU32_MACMU_9544 and tr_A0A2K5LIL6_A0A2K5LIL6_CERAT_9531 are exactly identical! WARNING: Sequences tr_H9FU32_H9FU32_MACMU_9544 and tr_A0A2K6BZB6_A0A2K6BZB6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A2Z3N4_A2Z3N4_ORYSI_39946 and tr_Q7XXN2_Q7XXN2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1QQW9_I1QQW9_ORYGL_4538 and tr_A0A0D3H9K3_A0A0D3H9K3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0EUH7_A0A0E0EUH7_9ORYZ_40149 and tr_A0A0E0B5Z4_A0A0E0B5Z4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_G1LDI9_G1LDI9_AILME_9646 and tr_A0A2U3ZB31_A0A2U3ZB31_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1LDI9_G1LDI9_AILME_9646 and tr_A0A2U3Y9A9_A0A2U3Y9A9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1LDI9_G1LDI9_AILME_9646 and tr_A0A2Y9J054_A0A2Y9J054_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1LDI9_G1LDI9_AILME_9646 and tr_A0A384CML7_A0A384CML7_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2K6W646_A0A2K6W646_ONCVO_6282 and tr_A0A182E103_A0A182E103_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A067FLE1_A0A067FLE1_CITSI_2711 and tr_V4U926_V4U926_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A096P039_A0A096P039_PAPAN_9555 and tr_A0A2K6B2M6_A0A2K6B2M6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D2REG1_A0A0D2REG1_GOSRA_29730 and tr_A0A1U8MLC5_A0A1U8MLC5_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A091J0M7_A0A091J0M7_EGRGA_188379 and tr_A0A087RH49_A0A087RH49_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0A0ANV3_A0A0A0ANV3_CHAVO_50402 and tr_A0A091I2S3_A0A091I2S3_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V1DE74_A0A0V1DE74_TRIBR_45882 and tr_A0A0V0VYT0_A0A0V0VYT0_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DE74_A0A0V1DE74_TRIBR_45882 and tr_A0A0V1LKD4_A0A0V1LKD4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DE74_A0A0V1DE74_TRIBR_45882 and tr_A0A0V1PG08_A0A0V1PG08_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DE74_A0A0V1DE74_TRIBR_45882 and tr_A0A0V0U6V3_A0A0V0U6V3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1DI89_A0A0V1DI89_TRIBR_45882 and tr_A0A0V0XAF7_A0A0V0XAF7_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1DI89_A0A0V1DI89_TRIBR_45882 and tr_A0A0V0V235_A0A0V0V235_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DI89_A0A0V1DI89_TRIBR_45882 and tr_A0A0V1L982_A0A0V1L982_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DI89_A0A0V1DI89_TRIBR_45882 and tr_A0A0V1PE13_A0A0V1PE13_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DI89_A0A0V1DI89_TRIBR_45882 and tr_A0A0V0U287_A0A0V0U287_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3XTN8_A0A1S3XTN8_TOBAC_4097 and tr_A0A1U7YJI0_A0A1U7YJI0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AA74_A0A1S4AA74_TOBAC_4097 and tr_A0A1U7YTV3_A0A1U7YTV3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2U4C6J2_A0A2U4C6J2_TURTR_9739 and tr_A0A2Y9NJT6_A0A2Y9NJT6_DELLE_9749 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/P15056/4_raxmlng_ancestral/P15056.raxml.reduced.phy Alignment comprises 1 partitions and 766 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 766 Gaps: 33.15 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15056/4_raxmlng_ancestral/P15056.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/P15056/3_mltree/P15056.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 192 / 15360 [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: -209076.190369 [00:00:00 -209076.190369] Initial branch length optimization [00:00:02 -207540.374950] Model parameter optimization (eps = 0.100000) [00:00:48] Tree #1, final logLikelihood: -207054.147824 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.109274,0.262189) (0.110392,0.271104) (0.336713,0.682282) (0.443621,1.604272) 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/P15056/4_raxmlng_ancestral/P15056.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15056/4_raxmlng_ancestral/P15056.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15056/4_raxmlng_ancestral/P15056.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15056/4_raxmlng_ancestral/P15056.raxml.log Analysis started: 03-Jun-2021 01:54:14 / finished: 03-Jun-2021 01:55:11 Elapsed time: 56.666 seconds Consumed energy: 3.809 Wh