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 02:49:37 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q5T1R4/2_msa/Q5T1R4_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q5T1R4/3_mltree/Q5T1R4.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q5T1R4/4_raxmlng_ancestral/Q5T1R4 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677777 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/Q5T1R4/2_msa/Q5T1R4_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 2406 sites WARNING: Sequences sp_Q8C208_IKZF4_MOUSE_10090 and tr_D4A636_D4A636_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XPF8_M3XPF8_MUSPF_9669 and tr_G1QDM6_G1QDM6_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3XPF8_M3XPF8_MUSPF_9669 and tr_J9NTQ0_J9NTQ0_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XPF8_M3XPF8_MUSPF_9669 and tr_M3WSR9_M3WSR9_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XPF8_M3XPF8_MUSPF_9669 and tr_A0A1U7UAC6_A0A1U7UAC6_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3XPF8_M3XPF8_MUSPF_9669 and tr_A0A2U3W197_A0A2U3W197_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XPF8_M3XPF8_MUSPF_9669 and tr_A0A2U3XBG7_A0A2U3XBG7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XPF8_M3XPF8_MUSPF_9669 and tr_A0A2Y9KXL4_A0A2Y9KXL4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3R7D9_G3R7D9_GORGO_9595 and tr_A0A2J8Q1G0_A0A2J8Q1G0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R7D9_G3R7D9_GORGO_9595 and sp_Q9H2S9_IKZF4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R7D9_G3R7D9_GORGO_9595 and tr_A0A2R9CIJ3_A0A2R9CIJ3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_H2QUK7_H2QUK7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and sp_Q13422_IKZF1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_F6YC72_F6YC72_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2R8MF47_A0A2R8MF47_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A096NWV9_A0A096NWV9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A0D9RTY8_A0A0D9RTY8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2K5NH61_A0A2K5NH61_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2K6C676_A0A2K6C676_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2K5ZPN0_A0A2K5ZPN0_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2R9B7I4_A0A2R9B7I4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_K7AFV7_K7AFV7_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_F7B8A3_F7B8A3_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A096MW48_A0A096MW48_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A2K6BT04_A0A2K6BT04_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A2K5YC92_A0A2K5YC92_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A2R9C8Y7_A0A2R9C8Y7_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5QD83_W5QD83_SHEEP_9940 and tr_A0A091CMP2_A0A091CMP2_FUKDA_885580 are exactly identical! WARNING: Sequences tr_F7GJV4_F7GJV4_MACMU_9544 and tr_G7NUE6_G7NUE6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7N7B0_G7N7B0_MACMU_9544 and tr_A0A2R8PL87_A0A2R8PL87_CALJA_9483 are exactly identical! WARNING: Sequences tr_G7N7B0_G7N7B0_MACMU_9544 and tr_G7PIG3_G7PIG3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7N7B0_G7N7B0_MACMU_9544 and tr_A0A0D9QYY9_A0A0D9QYY9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7N7B0_G7N7B0_MACMU_9544 and tr_A0A2K5LTX4_A0A2K5LTX4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7N7B0_G7N7B0_MACMU_9544 and tr_A0A2K6AQT5_A0A2K6AQT5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7N7B0_G7N7B0_MACMU_9544 and tr_A0A2K5YE94_A0A2K5YE94_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A044TQV9_A0A044TQV9_ONCVO_6282 and tr_A0A182E4H2_A0A182E4H2_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096NNM8_A0A096NNM8_PAPAN_9555 and tr_A0A2K6CMT3_A0A2K6CMT3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091J5J8_A0A091J5J8_EGRGA_188379 and tr_A0A091VQM4_A0A091VQM4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091J5J8_A0A091J5J8_EGRGA_188379 and tr_A0A091WL71_A0A091WL71_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091J5J8_A0A091J5J8_EGRGA_188379 and tr_A0A0A0ACN0_A0A0A0ACN0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1S3RNQ8_A0A1S3RNQ8_SALSA_8030 and tr_C0HBS6_C0HBS6_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1D1UEJ6_A0A1D1UEJ6_RAMVA_947166 and tr_A0A1D1UI44_A0A1D1UI44_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A226MZ88_A0A226MZ88_CALSU_9009 and tr_A0A226P0A3_A0A226P0A3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5P805_A0A2K5P805_CERAT_9531 and tr_A0A2K5Z9T2_A0A2K5Z9T2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2Y9MW95_A0A2Y9MW95_DELLE_9749 and tr_A0A2Y9EJC4_A0A2Y9EJC4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9MW95_A0A2Y9MW95_DELLE_9749 and tr_A0A384AKR0_A0A384AKR0_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 46 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/Q5T1R4/4_raxmlng_ancestral/Q5T1R4.raxml.reduced.phy Alignment comprises 1 partitions and 2406 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 2406 Gaps: 63.14 % Invariant sites: 0.12 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q5T1R4/4_raxmlng_ancestral/Q5T1R4.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/Q5T1R4/3_mltree/Q5T1R4.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 602 / 48160 [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: -636347.593626 [00:00:01 -636347.593626] Initial branch length optimization [00:00:16 -595660.336445] Model parameter optimization (eps = 0.100000) [00:06:57] Tree #1, final logLikelihood: -592315.660473 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.151477,1.147716) (0.105170,1.457417) (0.144752,0.320213) (0.598601,1.046640) 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/Q5T1R4/4_raxmlng_ancestral/Q5T1R4.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q5T1R4/4_raxmlng_ancestral/Q5T1R4.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q5T1R4/4_raxmlng_ancestral/Q5T1R4.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q5T1R4/4_raxmlng_ancestral/Q5T1R4.raxml.log Analysis started: 03-Jun-2021 02:49:37 / finished: 03-Jun-2021 02:57:03 Elapsed time: 445.968 seconds Consumed energy: 22.307 Wh