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 17-Jul-2021 07:19:19 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A087WSY6/2_msa/A0A087WSY6_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A087WSY6/3_mltree/A0A087WSY6.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A087WSY6/4_raxmlng_ancestral/A0A087WSY6 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626495559 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/A0A087WSY6/2_msa/A0A087WSY6_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 115 sites WARNING: Sequences tr_A0A140T8P9_A0A140T8P9_MOUSE_10090 and sp_P01638_KV5A6_MOUSE_10090 are exactly identical! WARNING: Sequences sp_P01654_KV3A1_MOUSE_10090 and sp_P01655_KV3A2_MOUSE_10090 are exactly identical! WARNING: Sequences sp_P01654_KV3A1_MOUSE_10090 and sp_P01656_KV3A3_MOUSE_10090 are exactly identical! WARNING: Sequences sp_P01654_KV3A1_MOUSE_10090 and sp_P03977_KV3A4_MOUSE_10090 are exactly identical! WARNING: Sequences sp_P01662_KV3AA_MOUSE_10090 and sp_P01663_KV3AB_MOUSE_10090 are exactly identical! WARNING: Sequences sp_P01665_KV3AD_MOUSE_10090 and sp_P01666_KV3AE_MOUSE_10090 are exactly identical! WARNING: Sequences sp_P01670_KV3AI_MOUSE_10090 and sp_P01671_KV3AJ_MOUSE_10090 are exactly identical! WARNING: Sequences tr_A0A2I2YMS6_A0A2I2YMS6_GORGO_9595 and tr_A0A2R9AK91_A0A2R9AK91_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3RYP8_A0A2I3RYP8_PANTR_9598 and tr_A0A2R9AL33_A0A2R9AL33_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SY06_A0A2I3SY06_PANTR_9598 and tr_A0A2R9AMP3_A0A2R9AMP3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TAX1_A0A2I3TAX1_PANTR_9598 and tr_A0A2R9AKE1_A0A2R9AKE1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R7U4_H2R7U4_PANTR_9598 and tr_A0A2R8ZT75_A0A2R8ZT75_PANPA_9597 are exactly identical! WARNING: Sequences tr_H0WN68_H0WN68_OTOGA_30611 and tr_H0XNM8_H0XNM8_OTOGA_30611 are exactly identical! WARNING: Sequences sp_A0A075B6P5_KV228_HUMAN_9606 and sp_P01615_KVD28_HUMAN_9606 are exactly identical! WARNING: Sequences sp_A0A087WW87_KV240_HUMAN_9606 and sp_P01614_KVD40_HUMAN_9606 are exactly identical! WARNING: Sequences sp_A0A0B4J2D9_KVD13_HUMAN_9606 and sp_P0DP09_KV113_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P01593_KVD33_HUMAN_9606 and sp_P01594_KV133_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P01597_KV139_HUMAN_9606 and sp_P04432_KVD39_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A1B8XXX6_A0A1B8XXX6_XENTR_8364 and tr_F6YDR4_F6YDR4_XENTR_8364 are exactly identical! WARNING: Sequences tr_A0A1B8XY36_A0A1B8XY36_XENTR_8364 and tr_F6TGA0_F6TGA0_XENTR_8364 are exactly identical! WARNING: Sequences tr_A0A1B8XZI5_A0A1B8XZI5_XENTR_8364 and tr_F7CRI8_F7CRI8_XENTR_8364 are exactly identical! WARNING: Sequences tr_A0A096MV46_A0A096MV46_PAPAN_9555 and tr_A0A2K6ALT7_A0A2K6ALT7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NGH2_A0A096NGH2_PAPAN_9555 and tr_A0A2K5NS08_A0A2K5NS08_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LZC8_A0A2I3LZC8_PAPAN_9555 and tr_A0A2K6B468_A0A2K6B468_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LZC8_A0A2I3LZC8_PAPAN_9555 and tr_A0A2K5XFL9_A0A2K5XFL9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3N776_A0A2I3N776_PAPAN_9555 and tr_A0A2K5NT28_A0A2K5NT28_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3N776_A0A2I3N776_PAPAN_9555 and tr_A0A2K6ALR0_A0A2K6ALR0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3NA91_A0A2I3NA91_PAPAN_9555 and tr_A0A2K5L3Y1_A0A2K5L3Y1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3NAX5_A0A2I3NAX5_PAPAN_9555 and tr_A0A2K6AT13_A0A2K6AT13_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5LXG6_A0A2K5LXG6_CERAT_9531 and tr_A0A2K5Z1U6_A0A2K5Z1U6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5Z859_A0A2K5Z859_MANLE_9568 and tr_A0A2K5ZVM6_A0A2K5ZVM6_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 31 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/A0A087WSY6/4_raxmlng_ancestral/A0A087WSY6.raxml.reduced.phy Alignment comprises 1 partitions and 115 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 115 Gaps: 4.69 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A087WSY6/4_raxmlng_ancestral/A0A087WSY6.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/A0A087WSY6/3_mltree/A0A087WSY6.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 29 / 2320 [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: -50208.607512 [00:00:00 -50208.607512] Initial branch length optimization [00:00:00 -50056.209938] Model parameter optimization (eps = 0.100000) [00:00:15] Tree #1, final logLikelihood: -49600.615080 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.270549,0.453372) (0.182839,0.514406) (0.459803,0.974290) (0.086810,3.862532) 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/A0A087WSY6/4_raxmlng_ancestral/A0A087WSY6.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A087WSY6/4_raxmlng_ancestral/A0A087WSY6.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A087WSY6/4_raxmlng_ancestral/A0A087WSY6.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A087WSY6/4_raxmlng_ancestral/A0A087WSY6.raxml.log Analysis started: 17-Jul-2021 07:19:19 / finished: 17-Jul-2021 07:19:36 Elapsed time: 16.795 seconds