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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 15:28:33 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99502/2_msa/Q99502_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99502/3_mltree/Q99502.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99502/4_raxmlng_ancestral/Q99502 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622636913 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99502/2_msa/Q99502_nogap_msa.fasta [00:00:00] Loaded alignment with 637 taxa and 592 sites WARNING: Sequences tr_B4Q4Y0_B4Q4Y0_DROSI_7240 and sp_Q05201_EYA_DROME_7227 are exactly identical! WARNING: Sequences tr_B4Q4Y0_B4Q4Y0_DROSI_7240 and tr_B4HXT6_B4HXT6_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1RX34_G1RX34_NOMLE_61853 and tr_G3RCE6_G3RCE6_GORGO_9595 are exactly identical! WARNING: Sequences tr_G3S1I3_G3S1I3_GORGO_9595 and tr_H2N8B5_H2N8B5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3S1I3_G3S1I3_GORGO_9595 and tr_K7D580_K7D580_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S1I3_G3S1I3_GORGO_9595 and sp_Q99504_EYA3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S1I3_G3S1I3_GORGO_9595 and tr_A0A2R9BMJ0_A0A2R9BMJ0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SKP8_G3SKP8_GORGO_9595 and tr_A0A2R9BSL8_A0A2R9BSL8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TVQ1_A0A2I3TVQ1_PANTR_9598 and tr_A0A2R8ZY72_A0A2R8ZY72_PANPA_9597 are exactly identical! WARNING: Sequences tr_C5HK62_C5HK62_SHEEP_9940 and tr_F1MGK4_F1MGK4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A0E0HJS4_A0A0E0HJS4_ORYNI_4536 and tr_I1PYV3_I1PYV3_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0HJS4_A0A0E0HJS4_ORYNI_4536 and tr_A0A0E0PSJ2_A0A0E0PSJ2_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0HJS4_A0A0E0HJS4_ORYNI_4536 and tr_A0A0E0A405_A0A0E0A405_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0HJS4_A0A0E0HJS4_ORYNI_4536 and tr_Q8H684_Q8H684_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F6SSJ2_F6SSJ2_MACMU_9544 and tr_G7PC08_G7PC08_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6SSJ2_F6SSJ2_MACMU_9544 and tr_A0A096NA76_A0A096NA76_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6SSJ2_F6SSJ2_MACMU_9544 and tr_A0A2K5LDF6_A0A2K5LDF6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6SSJ2_F6SSJ2_MACMU_9544 and tr_A0A2K6AXL0_A0A2K6AXL0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FR55_F7FR55_MACMU_9544 and tr_A0A2K5N024_A0A2K5N024_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FR55_F7FR55_MACMU_9544 and tr_A0A2K6A793_A0A2K6A793_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7MHZ5_G7MHZ5_MACMU_9544 and tr_G7NWV3_G7NWV3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MHZ5_G7MHZ5_MACMU_9544 and tr_A0A096NS28_A0A096NS28_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7MHZ5_G7MHZ5_MACMU_9544 and tr_A0A0D9S816_A0A0D9S816_CHLSB_60711 are exactly identical! WARNING: Sequences tr_W2QCQ1_W2QCQ1_PHYPN_761204 and tr_W2NG95_W2NG95_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A091IXS1_A0A091IXS1_EGRGA_188379 and tr_A0A091FKY5_A0A091FKY5_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091IXS1_A0A091IXS1_EGRGA_188379 and tr_A0A091IKX0_A0A091IKX0_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V1LPN6_A0A0V1LPN6_9BILA_6335 and tr_A0A0V1P6A0_A0A0V1P6A0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1LPN6_A0A0V1LPN6_9BILA_6335 and tr_A0A0V0UGQ8_A0A0V0UGQ8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S4AFR3_A0A1S4AFR3_TOBAC_4097 and tr_A0A1U7V8Q4_A0A1U7V8Q4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2D0PTG7_A0A2D0PTG7_ICTPU_7998 and tr_A0A2D0PVZ9_A0A2D0PVZ9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S3H6_A0A2D0S3H6_ICTPU_7998 and tr_A0A2D0S3K1_A0A2D0S3K1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S3H6_A0A2D0S3H6_ICTPU_7998 and tr_A0A2D0S4E3_A0A2D0S4E3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SJ84_A0A2D0SJ84_ICTPU_7998 and tr_A0A2D0SJU3_A0A2D0SJU3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SJ92_A0A2D0SJ92_ICTPU_7998 and tr_A0A2D0SJU7_A0A2D0SJU7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4BKZ8_A0A2U4BKZ8_TURTR_9739 and tr_A0A2U4BL05_A0A2U4BL05_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4BKZ8_A0A2U4BKZ8_TURTR_9739 and tr_A0A2Y9LDM9_A0A2Y9LDM9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BKZ8_A0A2U4BKZ8_TURTR_9739 and tr_A0A2Y9FDJ7_A0A2Y9FDJ7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4BKZ8_A0A2U4BKZ8_TURTR_9739 and tr_A0A383Z6Q8_A0A383Z6Q8_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9T208_A0A2Y9T208_PHYCD_9755 and tr_A0A384ACM8_A0A384ACM8_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 39 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99502/4_raxmlng_ancestral/Q99502.raxml.reduced.phy Alignment comprises 1 partitions and 592 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 592 Gaps: 22.33 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99502/4_raxmlng_ancestral/Q99502.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99502/3_mltree/Q99502.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 148 / 11840 [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: -105102.257642 [00:00:00 -105102.257642] Initial branch length optimization [00:00:01 -104340.320698] Model parameter optimization (eps = 0.100000) [00:00:52] Tree #1, final logLikelihood: -103793.749086 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.174390,2.022837) (0.107773,0.147239) (0.338942,0.435555) (0.378895,1.276715) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99502/4_raxmlng_ancestral/Q99502.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99502/4_raxmlng_ancestral/Q99502.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99502/4_raxmlng_ancestral/Q99502.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99502/4_raxmlng_ancestral/Q99502.raxml.log Analysis started: 02-Jun-2021 15:28:33 / finished: 02-Jun-2021 15:29:29 Elapsed time: 55.838 seconds