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 25-Jul-2021 22:01:26 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60658/2_msa/O60658_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60658/3_mltree/O60658.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60658/4_raxmlng_ancestral/O60658 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1627239686 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_300621/phylogeny-snakemake/results/O60658/2_msa/O60658_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 829 sites WARNING: Sequences tr_F1NDU5_F1NDU5_CHICK_9031 and tr_A0A226NGA0_A0A226NGA0_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NDU5_F1NDU5_CHICK_9031 and tr_A0A226PR46_A0A226PR46_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2I3GA09_A0A2I3GA09_NOMLE_61853 and tr_G3QV66_G3QV66_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GA09_A0A2I3GA09_NOMLE_61853 and tr_H2N752_H2N752_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3GA09_A0A2I3GA09_NOMLE_61853 and tr_F6QKI6_F6QKI6_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GA09_A0A2I3GA09_NOMLE_61853 and tr_U3DD68_U3DD68_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3GA09_A0A2I3GA09_NOMLE_61853 and tr_G7NW27_G7NW27_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3GA09_A0A2I3GA09_NOMLE_61853 and tr_A0A2I3MDK2_A0A2I3MDK2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GA09_A0A2I3GA09_NOMLE_61853 and tr_A0A2K6DQY6_A0A2K6DQY6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GCA2_A0A2I3GCA2_NOMLE_61853 and tr_K6ZBE9_K6ZBE9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GCA2_A0A2I3GCA2_NOMLE_61853 and sp_Q13946_PDE7A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YTP7_A0A2I2YTP7_GORGO_9595 and tr_A0A2K5XU66_A0A2K5XU66_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3RRZ5_A0A2I3RRZ5_PANTR_9598 and sp_Q08499_PDE4D_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RRZ5_A0A2I3RRZ5_PANTR_9598 and tr_F7GZT2_F7GZT2_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3RRZ5_A0A2I3RRZ5_PANTR_9598 and tr_A0A2K5LDG4_A0A2K5LDG4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3RRZ5_A0A2I3RRZ5_PANTR_9598 and tr_A0A2K6BBV4_A0A2K6BBV4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2J8NHG1_A0A2J8NHG1_PANTR_9598 and tr_A0A2R9AWP0_A0A2R9AWP0_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7ANH5_F7ANH5_HORSE_9796 and tr_A0A1U7TVG6_A0A1U7TVG6_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A158NNE0_A0A158NNE0_ATTCE_12957 and tr_F4WJP5_F4WJP5_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NNE0_A0A158NNE0_ATTCE_12957 and tr_A0A195AUW3_A0A195AUW3_9HYME_520822 are exactly identical! WARNING: Sequences tr_F7DG78_F7DG78_MACMU_9544 and tr_A0A2K5MVR4_A0A2K5MVR4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FU86_F7FU86_MACMU_9544 and tr_A0A2K6E528_A0A2K6E528_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MZG5_G7MZG5_MACMU_9544 and tr_G7PBY0_G7PBY0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MZG5_G7MZG5_MACMU_9544 and tr_A0A2K5NPA2_A0A2K5NPA2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MZG5_G7MZG5_MACMU_9544 and tr_A0A2K6CUX4_A0A2K6CUX4_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZLY6_H0ZLY6_TAEGU_59729 and tr_A0A093PXJ4_A0A093PXJ4_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZLY6_H0ZLY6_TAEGU_59729 and tr_A0A091W7M0_A0A091W7M0_OPIHO_30419 are exactly identical! WARNING: Sequences tr_W2R703_W2R703_PHYPN_761204 and tr_A0A0W8DWF1_A0A0W8DWF1_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2R703_W2R703_PHYPN_761204 and tr_W2GSS7_W2GSS7_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A2I0M599_A0A2I0M599_COLLI_8932 and tr_A0A1V4KRN8_A0A1V4KRN8_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3KF58_A0A1S3KF58_LINUN_7574 and tr_A0A1S3KFW4_A0A1S3KFW4_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A2K5N4R6_A0A2K5N4R6_CERAT_9531 and tr_A0A2K5ZUQ2_A0A2K5ZUQ2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4AX70_A0A2U4AX70_TURTR_9739 and tr_A0A383ZLU8_A0A383ZLU8_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 33 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60658/4_raxmlng_ancestral/O60658.raxml.reduced.phy Alignment comprises 1 partitions and 829 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 829 Gaps: 36.40 % Invariant sites: 0.24 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60658/4_raxmlng_ancestral/O60658.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_300621/phylogeny-snakemake/results/O60658/3_mltree/O60658.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 208 / 16640 [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: -228132.048310 [00:00:00 -228132.048310] Initial branch length optimization [00:00:02 -221767.322461] Model parameter optimization (eps = 0.100000) [00:01:51] Tree #1, final logLikelihood: -220980.139391 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.160789,0.343439) (0.142415,0.307808) (0.509589,0.786822) (0.187207,2.670764) 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_300621/phylogeny-snakemake/results/O60658/4_raxmlng_ancestral/O60658.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60658/4_raxmlng_ancestral/O60658.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60658/4_raxmlng_ancestral/O60658.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60658/4_raxmlng_ancestral/O60658.raxml.log Analysis started: 25-Jul-2021 22:01:26 / finished: 25-Jul-2021 22:03:24 Elapsed time: 118.304 seconds