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 02-Jun-2021 17:52:21 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00444/2_msa/O00444_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00444/3_mltree/O00444.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00444/4_raxmlng_ancestral/O00444 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622645541 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/O00444/2_msa/O00444_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 970 sites WARNING: Sequences tr_M3Y4C9_M3Y4C9_MUSPF_9669 and tr_A0A2Y9INE5_A0A2Y9INE5_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P52304_POLO_DROME_7227 and tr_B4IA77_B4IA77_DROSE_7238 are exactly identical! WARNING: Sequences tr_G3QW90_G3QW90_GORGO_9595 and tr_G2HFJ0_G2HFJ0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QW90_G3QW90_GORGO_9595 and sp_O14965_AURKA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QW90_G3QW90_GORGO_9595 and tr_A0A2R9ANX1_A0A2R9ANX1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RAD3_G3RAD3_GORGO_9595 and sp_Q5R4L1_PLK2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RAD3_G3RAD3_GORGO_9595 and tr_H2QQY0_H2QQY0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RAD3_G3RAD3_GORGO_9595 and sp_Q9NYY3_PLK2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RAD3_G3RAD3_GORGO_9595 and tr_H9EMK9_H9EMK9_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RAD3_G3RAD3_GORGO_9595 and tr_A0A096NBN2_A0A096NBN2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RAD3_G3RAD3_GORGO_9595 and tr_A0A0D9RUD3_A0A0D9RUD3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RAD3_G3RAD3_GORGO_9595 and tr_A0A2K5LLA4_A0A2K5LLA4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RAD3_G3RAD3_GORGO_9595 and tr_A0A2K6B577_A0A2K6B577_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RAD3_G3RAD3_GORGO_9595 and tr_A0A2K5XA48_A0A2K5XA48_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3RAD3_G3RAD3_GORGO_9595 and tr_A0A2R9BY27_A0A2R9BY27_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NQF2_H2NQF2_PONAB_9601 and sp_P53350_PLK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NQF2_H2NQF2_PONAB_9601 and tr_F7HSC1_F7HSC1_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2NQF2_H2NQF2_PONAB_9601 and tr_A0A2K5NUI3_A0A2K5NUI3_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2NQF2_H2NQF2_PONAB_9601 and tr_A0A2K6E282_A0A2K6E282_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2NQF2_H2NQF2_PONAB_9601 and tr_A0A2K5Z4L7_A0A2K5Z4L7_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2PYW5_H2PYW5_PANTR_9598 and tr_A0A2R9BEM8_A0A2R9BEM8_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7BZR6_K7BZR6_PANTR_9598 and tr_A0A2R9AC53_A0A2R9AC53_PANPA_9597 are exactly identical! WARNING: Sequences tr_E5RZA9_E5RZA9_TRISP_6334 and tr_A0A0V0ZIS7_A0A0V0ZIS7_9BILA_990121 are exactly identical! WARNING: Sequences tr_F4PCH9_F4PCH9_BATDJ_684364 and tr_A0A177WYS4_A0A177WYS4_BATDE_403673 are exactly identical! WARNING: Sequences tr_W2PNT8_W2PNT8_PHYPN_761204 and tr_A0A0W8CBA6_A0A0W8CBA6_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PNT8_W2PNT8_PHYPN_761204 and tr_W2KG09_W2KG09_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QAX1_W2QAX1_PHYPN_761204 and tr_W2L8X5_W2L8X5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A044U7C5_A0A044U7C5_ONCVO_6282 and tr_A0A182E281_A0A182E281_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096NNK5_A0A096NNK5_PAPAN_9555 and tr_A0A2K5M130_A0A2K5M130_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9RS62_A0A0D9RS62_CHLSB_60711 and tr_A0A2K6AZG6_A0A2K6AZG6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0V1CLM4_A0A0V1CLM4_TRIBR_45882 and tr_A0A0V0WGT7_A0A0V0WGT7_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CLM4_A0A0V1CLM4_TRIBR_45882 and tr_A0A0V0V2L0_A0A0V0V2L0_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CLM4_A0A0V1CLM4_TRIBR_45882 and tr_A0A0V1LN00_A0A0V1LN00_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CLM4_A0A0V1CLM4_TRIBR_45882 and tr_A0A0V1NUB6_A0A0V1NUB6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CLM4_A0A0V1CLM4_TRIBR_45882 and tr_A0A0V0TZJ8_A0A0V0TZJ8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0UYR8_A0A0V0UYR8_9BILA_181606 and tr_A0A0V1LP83_A0A0V1LP83_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0UYR8_A0A0V0UYR8_9BILA_181606 and tr_A0A0V0TN46_A0A0V0TN46_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1MQG4_A0A0V1MQG4_9BILA_268474 and tr_A0A0V1GXE3_A0A0V1GXE3_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A226N3J5_A0A226N3J5_CALSU_9009 and tr_A0A226PJ70_A0A226PJ70_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NM44_A0A226NM44_CALSU_9009 and tr_A0A226PQ69_A0A226PQ69_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NMH0_A0A226NMH0_CALSU_9009 and tr_A0A226PGU7_A0A226PGU7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3V4Z5_A0A2U3V4Z5_TURTR_9739 and tr_A0A2Y9QCE6_A0A2Y9QCE6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V4Z5_A0A2U3V4Z5_TURTR_9739 and tr_A0A2Y9ELJ6_A0A2Y9ELJ6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3V4Z5_A0A2U3V4Z5_TURTR_9739 and tr_A0A384ADF4_A0A384ADF4_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4AXQ0_A0A2U4AXQ0_TURTR_9739 and tr_A0A383ZM20_A0A383ZM20_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 45 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/O00444/4_raxmlng_ancestral/O00444.raxml.reduced.phy Alignment comprises 1 partitions and 970 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 970 Gaps: 48.46 % Invariant sites: 0.31 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00444/4_raxmlng_ancestral/O00444.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/O00444/3_mltree/O00444.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 243 / 19440 [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: -346489.364705 [00:00:00 -346489.364705] Initial branch length optimization [00:00:04 -326143.742260] Model parameter optimization (eps = 0.100000) [00:01:29] Tree #1, final logLikelihood: -325574.952841 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.084088,0.166849) (0.108495,0.238627) (0.294630,0.651775) (0.512787,1.497790) 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/O00444/4_raxmlng_ancestral/O00444.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00444/4_raxmlng_ancestral/O00444.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00444/4_raxmlng_ancestral/O00444.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00444/4_raxmlng_ancestral/O00444.raxml.log Analysis started: 02-Jun-2021 17:52:21 / finished: 02-Jun-2021 17:54:00 Elapsed time: 99.073 seconds Consumed energy: 6.223 Wh