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 01:50:19 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q53EL9/2_msa/Q53EL9_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q53EL9/3_mltree/Q53EL9.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q53EL9/4_raxmlng_ancestral/Q53EL9 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674219 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/Q53EL9/2_msa/Q53EL9_nogap_msa.fasta [00:00:00] Loaded alignment with 963 taxa and 994 sites WARNING: Sequences tr_A0A1D5PSP2_A0A1D5PSP2_CHICK_9031 and tr_U3I4H5_U3I4H5_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1D5PSP2_A0A1D5PSP2_CHICK_9031 and tr_A0A091EWE8_A0A091EWE8_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A1D5PSP2_A0A1D5PSP2_CHICK_9031 and tr_A0A091J880_A0A091J880_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A1D5PSP2_A0A1D5PSP2_CHICK_9031 and tr_A0A091UUM2_A0A091UUM2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5PSP2_A0A1D5PSP2_CHICK_9031 and tr_A0A087RJX0_A0A087RJX0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1D5PSP2_A0A1D5PSP2_CHICK_9031 and tr_A0A093K7G0_A0A093K7G0_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A1D5PSP2_A0A1D5PSP2_CHICK_9031 and tr_A0A099ZRA1_A0A099ZRA1_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A1D5PSP2_A0A1D5PSP2_CHICK_9031 and tr_A0A091FF50_A0A091FF50_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5PSP2_A0A1D5PSP2_CHICK_9031 and tr_A0A0A0AGK6_A0A0A0AGK6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1D5PSP2_A0A1D5PSP2_CHICK_9031 and tr_A0A093FWM3_A0A093FWM3_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A1D5PSP2_A0A1D5PSP2_CHICK_9031 and tr_A0A091HRQ3_A0A091HRQ3_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A1L1RW02_A0A1L1RW02_CHICK_9031 and sp_P79795_NRP1_CHICK_9031 are exactly identical! WARNING: Sequences tr_G3R279_G3R279_GORGO_9595 and sp_O60462_NRP2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R279_G3R279_GORGO_9595 and tr_A0A2R9C6T9_A0A2R9C6T9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PPE1_H2PPE1_PONAB_9601 and tr_G5AUB1_G5AUB1_HETGA_10181 are exactly identical! WARNING: Sequences tr_H2PPE1_H2PPE1_PONAB_9601 and tr_G7PCC2_G7PCC2_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2PPE1_H2PPE1_PONAB_9601 and tr_A0A0D9RWQ9_A0A0D9RWQ9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2QWL4_H2QWL4_PANTR_9598 and tr_A0A2R9C8Y9_A0A2R9C8Y9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7G9W1_F7G9W1_MACMU_9544 and tr_G7PL91_G7PL91_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7G9W1_F7G9W1_MACMU_9544 and tr_A0A096N6G9_A0A096N6G9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7G9W1_F7G9W1_MACMU_9544 and tr_A0A2K6D5X4_A0A2K6D5X4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7G9W1_F7G9W1_MACMU_9544 and tr_A0A2K5Z5G7_A0A2K5Z5G7_MANLE_9568 are exactly identical! WARNING: Sequences tr_U3JXA7_U3JXA7_FICAL_59894 and tr_A0A218V6Z8_A0A218V6Z8_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A1S3IED8_A0A1S3IED8_LINUN_7574 and tr_A0A1S3IGC2_A0A1S3IGC2_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A2K6CPR3_A0A2K6CPR3_MACNE_9545 and tr_A0A2K5Z8Z5_A0A2K5Z8Z5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4BN37_A0A2U4BN37_TURTR_9739 and tr_A0A2U4BNF8_A0A2U4BNF8_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4BN42_A0A2U4BN42_TURTR_9739 and tr_A0A2U4BN43_A0A2U4BN43_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4BN42_A0A2U4BN42_TURTR_9739 and tr_A0A2U4BN98_A0A2U4BN98_TURTR_9739 are exactly identical! WARNING: Duplicate sequences found: 28 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/Q53EL9/4_raxmlng_ancestral/Q53EL9.raxml.reduced.phy Alignment comprises 1 partitions and 994 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 994 Gaps: 47.19 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q53EL9/4_raxmlng_ancestral/Q53EL9.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/Q53EL9/3_mltree/Q53EL9.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 249 / 19920 [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: -353760.343514 [00:00:00 -353760.343514] Initial branch length optimization [00:00:02 -307077.543454] Model parameter optimization (eps = 0.100000) [00:01:24] Tree #1, final logLikelihood: -306129.794715 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.054411,0.188217) (0.065993,0.519812) (0.475549,0.792445) (0.404047,1.432031) 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/Q53EL9/4_raxmlng_ancestral/Q53EL9.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q53EL9/4_raxmlng_ancestral/Q53EL9.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q53EL9/4_raxmlng_ancestral/Q53EL9.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q53EL9/4_raxmlng_ancestral/Q53EL9.raxml.log Analysis started: 03-Jun-2021 01:50:19 / finished: 03-Jun-2021 01:51:51 Elapsed time: 92.577 seconds Consumed energy: 8.097 Wh