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 18:34:20 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P31645/2_msa/P31645_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P31645/3_mltree/P31645.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P31645/4_raxmlng_ancestral/P31645 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622648060 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/P31645/2_msa/P31645_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 630 sites WARNING: Sequences tr_B4QI04_B4QI04_DROSI_7240 and sp_Q7K4Y6_DAT_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QI04_B4QI04_DROSI_7240 and tr_B4HSZ4_B4HSZ4_DROSE_7238 are exactly identical! WARNING: Sequences sp_P31648_SC6A1_MOUSE_10090 and sp_P23978_SC6A1_RAT_10116 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_H2PA22_H2PA22_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_H2QM23_H2QM23_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and sp_P30531_SC6A1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_F6WVM8_F6WVM8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_G7NYT4_G7NYT4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A096NQ20_A0A096NQ20_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A0D9RC09_A0A0D9RC09_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2K6A0C9_A0A2K6A0C9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2R9CH47_A0A2R9CH47_PANPA_9597 are exactly identical! WARNING: Sequences tr_B5DZ75_B5DZ75_DROPS_46245 and tr_B4H683_B4H683_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q291U3_Q291U3_DROPS_46245 and tr_B4GA93_B4GA93_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2RKV9_E2RKV9_CANLF_9615 and tr_A0A2I2UPJ1_A0A2I2UPJ1_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2RKV9_E2RKV9_CANLF_9615 and tr_A0A2U3YMF9_A0A2U3YMF9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2J8LIN5_A0A2J8LIN5_PANTR_9598 and tr_A0A2R9ADR4_A0A2R9ADR4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8MWT0_A0A2J8MWT0_PANTR_9598 and sp_P23975_SC6A2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q3A9_H2Q3A9_PANTR_9598 and tr_A0A2R9AHV1_A0A2R9AHV1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QQL1_H2QQL1_PANTR_9598 and tr_A0A2R8ZUK6_A0A2R8ZUK6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NPD8_A0A158NPD8_ATTCE_12957 and tr_F4WH84_F4WH84_ACREC_103372 are exactly identical! WARNING: Sequences tr_F7F7H9_F7F7H9_MACMU_9544 and tr_G7PQK0_G7PQK0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7F7H9_F7F7H9_MACMU_9544 and tr_A0A096NG10_A0A096NG10_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7F7H9_F7F7H9_MACMU_9544 and tr_A0A2K6ECY9_A0A2K6ECY9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F7H9_F7F7H9_MACMU_9544 and tr_A0A2K5YI07_A0A2K5YI07_MANLE_9568 are exactly identical! WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A2K5KJJ7_A0A2K5KJJ7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A2K6C6Z6_A0A2K6C6Z6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A2K5Z263_A0A2K5Z263_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A087XTR0_A0A087XTR0_POEFO_48698 and tr_A0A087YDV2_A0A087YDV2_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A096MYM4_A0A096MYM4_PAPAN_9555 and tr_A0A2K5LFH9_A0A2K5LFH9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N2F3_A0A096N2F3_PAPAN_9555 and tr_A0A2K6BWY5_A0A2K6BWY5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LMR0_A0A2I3LMR0_PAPAN_9555 and tr_A0A2K5XWL6_A0A2K5XWL6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151NIH4_A0A151NIH4_ALLMI_8496 and tr_A0A1U7SBY4_A0A1U7SBY4_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091J5I8_A0A091J5I8_EGRGA_188379 and tr_A0A099ZZS3_A0A099ZZS3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VSV1_A0A091VSV1_NIPNI_128390 and tr_A0A087RH38_A0A087RH38_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VSV1_A0A091VSV1_NIPNI_128390 and tr_A0A0A0ATB2_A0A0A0ATB2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1LM53_A0A0V1LM53_9BILA_6335 and tr_A0A0V1PDQ7_A0A0V1PDQ7_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1I7TEH4_A0A1I7TEH4_9PELO_1561998 and tr_A0A1I7TEH5_A0A1I7TEH5_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2D0RWR4_A0A2D0RWR4_ICTPU_7998 and tr_A0A2D0RYA2_A0A2D0RYA2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KZH8_A0A2K5KZH8_CERAT_9531 and tr_A0A2K6BVQ8_A0A2K6BVQ8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5M1V4_A0A2K5M1V4_CERAT_9531 and tr_A0A2K5XEV8_A0A2K5XEV8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4B4F4_A0A2U4B4F4_TURTR_9739 and tr_A0A2Y9LN82_A0A2Y9LN82_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 42 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/P31645/4_raxmlng_ancestral/P31645.raxml.reduced.phy Alignment comprises 1 partitions and 630 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 630 Gaps: 11.12 % Invariant sites: 0.79 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P31645/4_raxmlng_ancestral/P31645.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/P31645/3_mltree/P31645.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 158 / 12640 [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: -198689.542027 [00:00:00 -198689.542027] Initial branch length optimization [00:00:01 -195686.394988] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -195055.407222 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.239046,0.286817) (0.327058,0.417451) (0.243505,1.130986) (0.190391,2.728626) 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/P31645/4_raxmlng_ancestral/P31645.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P31645/4_raxmlng_ancestral/P31645.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P31645/4_raxmlng_ancestral/P31645.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P31645/4_raxmlng_ancestral/P31645.raxml.log Analysis started: 02-Jun-2021 18:34:20 / finished: 02-Jun-2021 18:35:08 Elapsed time: 48.205 seconds Consumed energy: 3.261 Wh