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 12-Jul-2021 18:07:08 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/2_msa/Q8N1P7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/3_mltree/Q8N1P7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/4_raxmlng_ancestral/Q8N1P7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102428 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/300621_run/phylogeny-snakemake/results/Q8N1P7/2_msa/Q8N1P7_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 1661 sites WARNING: Sequences sp_P62696_CRBB2_MOUSE_10090 and sp_P62697_CRBB2_RAT_10116 are exactly identical! WARNING: Sequences sp_P62696_CRBB2_MOUSE_10090 and tr_A0A1U7Q218_A0A1U7Q218_MESAU_10036 are exactly identical! WARNING: Sequences sp_P62696_CRBB2_MOUSE_10090 and sp_P62698_CRBB2_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3YC57_M3YC57_MUSPF_9669 and tr_A0A2Y9K901_A0A2Y9K901_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and sp_P43320_CRBB2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and tr_A0A096NW62_A0A096NW62_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and tr_A0A0D9RCT3_A0A0D9RCT3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and tr_A0A2K5NA26_A0A2K5NA26_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RCE9_G3RCE9_GORGO_9595 and sp_P22914_CRYGS_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RMA8_G3RMA8_GORGO_9595 and tr_H2QJB0_H2QJB0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RMA8_G3RMA8_GORGO_9595 and sp_P07320_CRGD_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and tr_H2QJB1_H2QJB1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SGF7_G3SGF7_GORGO_9595 and tr_H2R0F6_H2R0F6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SGF7_G3SGF7_GORGO_9595 and tr_A0A2R9A076_A0A2R9A076_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q2LEC2_CRBB2_CANLF_9615 and tr_M3WJG9_M3WJG9_FELCA_9685 are exactly identical! WARNING: Sequences tr_A7KK31_A7KK31_PANTR_9598 and sp_P11844_CRGA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A7KK31_A7KK31_PANTR_9598 and tr_A7KK28_A7KK28_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QLE9_H2QLE9_PANTR_9598 and tr_A0A2R9A3H6_A0A2R9A3H6_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5QCG5_W5QCG5_SHEEP_9940 and sp_P02522_CRBB2_BOVIN_9913 are exactly identical! WARNING: Sequences sp_A3RLD8_CRGC_MACMU_9544 and tr_G7PLA8_G7PLA8_MACFA_9541 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_A0A2I3N8B8_A0A2I3N8B8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_A0A2K5NYX4_A0A2K5NYX4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_A0A2K6A4K3_A0A2K6A4K3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_G7NYM3_G7NYM3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A096NCK3_A0A096NCK3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A0D9RNN2_A0A0D9RNN2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A2K5P3E0_A0A2K5P3E0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A2K6C2J9_A0A2K6C2J9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A2K5XZH8_A0A2K5XZH8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_G7PLA7_G7PLA7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_A0A2I3MTV9_A0A2I3MTV9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_A0A2K5MVY4_A0A2K5MVY4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_A0A2K5XTU2_A0A2K5XTU2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7F0F8_F7F0F8_MACMU_9544 and tr_G7PHG1_G7PHG1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7F0F8_F7F0F8_MACMU_9544 and tr_A0A2K6CA33_A0A2K6CA33_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F0G3_F7F0G3_MACMU_9544 and tr_G7PHG2_G7PHG2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7F0G3_F7F0G3_MACMU_9544 and tr_A0A096NRG8_A0A096NRG8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7F0G3_F7F0G3_MACMU_9544 and tr_A0A2K6CN04_A0A2K6CN04_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F0G3_F7F0G3_MACMU_9544 and tr_A0A2K5YFB3_A0A2K5YFB3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7PLA9_G7PLA9_MACFA_9541 and tr_A0A0D9RCE9_A0A0D9RCE9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A087YK63_A0A087YK63_POEFO_48698 and tr_A0A096MA92_A0A096MA92_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A2I3MKU1_A0A2I3MKU1_PAPAN_9555 and tr_A0A2K5MMW1_A0A2K5MMW1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MRW5_A0A2I3MRW5_PAPAN_9555 and tr_A0A2K5MJV9_A0A2K5MJV9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MRW5_A0A2I3MRW5_PAPAN_9555 and tr_A0A2K6B305_A0A2K6B305_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3MRW5_A0A2I3MRW5_PAPAN_9555 and tr_A0A2K6AKB7_A0A2K6AKB7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151NSD4_A0A151NSD4_ALLMI_8496 and tr_A0A1U7RC16_A0A1U7RC16_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A1S3PN29_A0A1S3PN29_SALSA_8030 and tr_A0A060WPA1_A0A060WPA1_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1L8HNK9_A0A1L8HNK9_XENLA_8355 and tr_A0A1L8HNL8_A0A1L8HNL8_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A2K5N1A1_A0A2K5N1A1_CERAT_9531 and tr_A0A2K5XZP1_A0A2K5XZP1_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 49 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/4_raxmlng_ancestral/Q8N1P7.raxml.reduced.phy Alignment comprises 1 partitions and 1661 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1661 Gaps: 74.33 % Invariant sites: 0.30 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/4_raxmlng_ancestral/Q8N1P7.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/300621_run/phylogeny-snakemake/results/Q8N1P7/3_mltree/Q8N1P7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 416 / 33280 [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: -303640.141056 [00:00:00 -303640.141056] Initial branch length optimization [00:00:03 -263127.094168] Model parameter optimization (eps = 0.100000) [00:01:23] Tree #1, final logLikelihood: -262383.511474 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.070771,0.207942) (0.094256,0.302622) (0.300331,0.581574) (0.534642,1.462839) 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/300621_run/phylogeny-snakemake/results/Q8N1P7/4_raxmlng_ancestral/Q8N1P7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/4_raxmlng_ancestral/Q8N1P7.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/4_raxmlng_ancestral/Q8N1P7.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/4_raxmlng_ancestral/Q8N1P7.raxml.log Analysis started: 12-Jul-2021 18:07:08 / finished: 12-Jul-2021 18:08:46 Elapsed time: 98.111 seconds Consumed energy: 7.223 Wh