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 02-Jun-2021 18:20:39 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HD43/2_msa/Q9HD43_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HD43/3_mltree/Q9HD43.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HD43/4_raxmlng_ancestral/Q9HD43 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647239 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/020621_run/phylogeny-snakemake/results/Q9HD43/2_msa/Q9HD43_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1115 sites WARNING: Sequences tr_F1P3J3_F1P3J3_CHICK_9031 and sp_Q9W6V5_PTPRJ_CHICK_9031 are exactly identical! WARNING: Sequences tr_G1PXE7_G1PXE7_MYOLU_59463 and sp_O14522_PTPRT_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1PXE7_G1PXE7_MYOLU_59463 and tr_F6PVC0_F6PVC0_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3S6G3_G3S6G3_GORGO_9595 and tr_A0A2I3SQY6_A0A2I3SQY6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S6G3_G3S6G3_GORGO_9595 and tr_F6V5S0_F6V5S0_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3S6G3_G3S6G3_GORGO_9595 and tr_G7P370_G7P370_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3S6G3_G3S6G3_GORGO_9595 and tr_A0A2I3LW03_A0A2I3LW03_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S6G3_G3S6G3_GORGO_9595 and tr_A0A0D9RV87_A0A0D9RV87_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3S6G3_G3S6G3_GORGO_9595 and tr_A0A2K5ZG26_A0A2K5ZG26_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3S6G3_G3S6G3_GORGO_9595 and tr_A0A2R8ZP60_A0A2R8ZP60_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SMH2_A0A2I3SMH2_PANTR_9598 and tr_A0A2R9B8C3_A0A2R9B8C3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NAA8_A0A158NAA8_ATTCE_12957 and tr_A0A195BJD7_A0A195BJD7_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A1D5RCM2_A0A1D5RCM2_MACMU_9544 and tr_G7PI16_G7PI16_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RET9_A0A1D5RET9_MACMU_9544 and tr_A0A2I3NB73_A0A2I3NB73_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5RET9_A0A1D5RET9_MACMU_9544 and tr_A0A2K5NRK6_A0A2K5NRK6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5RET9_A0A1D5RET9_MACMU_9544 and tr_A0A2K6EBP7_A0A2K6EBP7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5RET9_A0A1D5RET9_MACMU_9544 and tr_A0A2K6AAG8_A0A2K6AAG8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6TLA3_F6TLA3_MACMU_9544 and tr_A0A2I3NAL0_A0A2I3NAL0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3N9W3_A0A2I3N9W3_PAPAN_9555 and tr_A0A0D9R9K5_A0A0D9R9K5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A091KAC9_A0A091KAC9_EGRGA_188379 and tr_A0A091WZA0_A0A091WZA0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A2I0M2A7_A0A2I0M2A7_COLLI_8932 and tr_A0A1V4KMY5_A0A1V4KMY5_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3HGB1_A0A1S3HGB1_LINUN_7574 and tr_A0A1S3HGB4_A0A1S3HGB4_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3HGB1_A0A1S3HGB1_LINUN_7574 and tr_A0A1S3HGB9_A0A1S3HGB9_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3HGB1_A0A1S3HGB1_LINUN_7574 and tr_A0A1S3HHY9_A0A1S3HHY9_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1W4V7G9_A0A1W4V7G9_DROFC_30025 and tr_A0A1W4WAG1_A0A1W4WAG1_DROFC_30025 are exactly identical! WARNING: Sequences tr_A0A226NB73_A0A226NB73_CALSU_9009 and tr_A0A226P275_A0A226P275_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PV98_A0A2D0PV98_ICTPU_7998 and tr_A0A2D0PYE1_A0A2D0PYE1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PV98_A0A2D0PV98_ICTPU_7998 and tr_A0A2D0PZB7_A0A2D0PZB7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PVC0_A0A2D0PVC0_ICTPU_7998 and tr_A0A2D0PYG0_A0A2D0PYG0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RWZ5_A0A2D0RWZ5_ICTPU_7998 and tr_A0A2D0RXW6_A0A2D0RXW6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2Y9PNW4_A0A2Y9PNW4_DELLE_9749 and tr_A0A2Y9SAW7_A0A2Y9SAW7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9PNW4_A0A2Y9PNW4_DELLE_9749 and tr_A0A384B8A1_A0A384B8A1_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 32 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HD43/4_raxmlng_ancestral/Q9HD43.raxml.reduced.phy Alignment comprises 1 partitions and 1115 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1115 Gaps: 35.17 % Invariant sites: 2.42 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HD43/4_raxmlng_ancestral/Q9HD43.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/020621_run/phylogeny-snakemake/results/Q9HD43/3_mltree/Q9HD43.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 279 / 22320 [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: -391145.635589 [00:00:00 -391145.635589] Initial branch length optimization [00:00:04 -350770.337958] Model parameter optimization (eps = 0.100000) [00:02:50] Tree #1, final logLikelihood: -350182.172087 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.096682,0.194886) (0.127465,0.338365) (0.424927,0.861991) (0.350926,1.629246) 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/020621_run/phylogeny-snakemake/results/Q9HD43/4_raxmlng_ancestral/Q9HD43.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HD43/4_raxmlng_ancestral/Q9HD43.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HD43/4_raxmlng_ancestral/Q9HD43.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HD43/4_raxmlng_ancestral/Q9HD43.raxml.log Analysis started: 02-Jun-2021 18:20:39 / finished: 02-Jun-2021 18:23:40 Elapsed time: 181.478 seconds Consumed energy: 8.777 Wh