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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 12-Jul-2021 17:14:32 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14843/2_msa/O14843_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14843/3_mltree/O14843.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14843/4_raxmlng_ancestral/O14843 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099272 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/O14843/2_msa/O14843_nogap_msa.fasta [00:00:00] Loaded alignment with 530 taxa and 346 sites WARNING: Sequences sp_Q8BLG2_LPAR4_MOUSE_10090 and tr_G3ICW4_G3ICW4_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q8BLG2_LPAR4_MOUSE_10090 and tr_D3ZHA3_D3ZHA3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BLG2_LPAR4_MOUSE_10090 and tr_A0A3Q0CDJ3_A0A3Q0CDJ3_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q8BLG2_LPAR4_MOUSE_10090 and tr_D5MRP4_D5MRP4_MESAU_10036 are exactly identical! WARNING: Sequences tr_G1SBK7_G1SBK7_NOMLE_61853 and tr_H2PW41_H2PW41_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1SBK7_G1SBK7_NOMLE_61853 and sp_Q99677_LPAR4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NG89_H2NG89_PONAB_9601 and tr_H2RGA1_H2RGA1_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NG89_H2NG89_PONAB_9601 and tr_A0A2R8ZEH5_A0A2R8ZEH5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1TG91_G1TG91_RABIT_9986 and tr_A0A1S3G6C1_A0A1S3G6C1_DIPOR_10020 are exactly identical! WARNING: Sequences tr_H2QG25_H2QG25_PANTR_9598 and tr_A0A2R8ZS24_A0A2R8ZS24_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R4U2_H2R4U2_PANTR_9598 and tr_A0A2R8ZAQ1_A0A2R8ZAQ1_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5P7T0_W5P7T0_SHEEP_9940 and tr_A4IFV1_A4IFV1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F6W3L4_F6W3L4_MACMU_9544 and tr_G7PX90_G7PX90_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7B7B1_F7B7B1_MACMU_9544 and tr_G7Q339_G7Q339_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7B7B1_F7B7B1_MACMU_9544 and tr_A0A096MLK8_A0A096MLK8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7B7B1_F7B7B1_MACMU_9544 and tr_A0A0D9SAL6_A0A0D9SAL6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7B7B1_F7B7B1_MACMU_9544 and tr_A0A2K5NV18_A0A2K5NV18_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7B7B1_F7B7B1_MACMU_9544 and tr_A0A2K6B3U1_A0A2K6B3U1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B7B1_F7B7B1_MACMU_9544 and tr_A0A2K5XRV2_A0A2K5XRV2_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YWI6_H0YWI6_TAEGU_59729 and tr_A0A091EAS0_A0A091EAS0_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A2I3N538_A0A2I3N538_PAPAN_9555 and tr_A0A2K5XFW5_A0A2K5XFW5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1U7Q260_A0A1U7Q260_MESAU_10036 and sp_Q76JU8_FFAR1_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2K5KNA6_A0A2K5KNA6_CERAT_9531 and tr_A0A2K6B121_A0A2K6B121_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5KNA6_A0A2K5KNA6_CERAT_9531 and tr_A0A2K5XT84_A0A2K5XT84_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5KQ90_A0A2K5KQ90_CERAT_9531 and tr_A0A2K6AZP9_A0A2K6AZP9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2U3V3Q4_A0A2U3V3Q4_TURTR_9739 and tr_A0A2Y9P2S6_A0A2Y9P2S6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V3Q4_A0A2U3V3Q4_TURTR_9739 and tr_A0A2Y9FHD8_A0A2Y9FHD8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3V3Q4_A0A2U3V3Q4_TURTR_9739 and tr_A0A384APZ3_A0A384APZ3_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4C4I0_A0A2U4C4I0_TURTR_9739 and tr_A0A2Y9M944_A0A2Y9M944_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 29 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/O14843/4_raxmlng_ancestral/O14843.raxml.reduced.phy Alignment comprises 1 partitions and 346 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 346 Gaps: 17.10 % Invariant sites: 0.29 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14843/4_raxmlng_ancestral/O14843.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/O14843/3_mltree/O14843.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 87 / 6960 [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: -103381.130619 [00:00:00 -103381.130619] Initial branch length optimization [00:00:00 -101274.104325] Model parameter optimization (eps = 0.100000) [00:00:22] Tree #1, final logLikelihood: -101003.192431 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.176281,0.361667) (0.243932,0.529675) (0.352420,0.896643) (0.227368,2.159698) 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/O14843/4_raxmlng_ancestral/O14843.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14843/4_raxmlng_ancestral/O14843.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14843/4_raxmlng_ancestral/O14843.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14843/4_raxmlng_ancestral/O14843.raxml.log Analysis started: 12-Jul-2021 17:14:32 / finished: 12-Jul-2021 17:14:56 Elapsed time: 23.957 seconds Consumed energy: 1.845 Wh