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 03-Jun-2021 14:59:56 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z2Y5/2_msa/Q7Z2Y5_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z2Y5/3_mltree/Q7Z2Y5.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z2Y5/4_raxmlng_ancestral/Q7Z2Y5 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622721596 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/Q7Z2Y5/2_msa/Q7Z2Y5_nogap_msa.fasta [00:00:00] Loaded alignment with 981 taxa and 1582 sites WARNING: Sequences tr_M3Z0C5_M3Z0C5_MUSPF_9669 and tr_A0A2Y9JFN6_A0A2Y9JFN6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1R076_G1R076_NOMLE_61853 and tr_H2PBZ9_H2PBZ9_PONAB_9601 are exactly identical! WARNING: Sequences tr_J3K3K4_J3K3K4_COCIM_246410 and tr_A0A0J6YDX7_A0A0J6YDX7_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6Q8M4_B6Q8M4_TALMQ_441960 and tr_A0A093VC69_A0A093VC69_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3QX47_G3QX47_GORGO_9595 and sp_Q9UKE5_TNIK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QX47_G3QX47_GORGO_9595 and tr_A0A2R9BG34_A0A2R9BG34_PANPA_9597 are exactly identical! WARNING: Sequences tr_B8MW16_B8MW16_ASPFN_332952 and tr_Q2UT83_Q2UT83_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8MW16_B8MW16_ASPFN_332952 and tr_A0A1S9DWU0_A0A1S9DWU0_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A2I3RZ34_A0A2I3RZ34_PANTR_9598 and tr_A0A2R9C950_A0A2R9C950_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FUN4_F9FUN4_FUSOF_660025 and tr_X0BHI6_X0BHI6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FUN4_F9FUN4_FUSOF_660025 and tr_A0A2H3TRR7_A0A2H3TRR7_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A2R1E1_A2R1E1_ASPNC_425011 and tr_A0A319B9L1_A0A319B9L1_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F6XGR9_F6XGR9_MACMU_9544 and tr_G7NZE8_G7NZE8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6XGR9_F6XGR9_MACMU_9544 and tr_A0A096MXB6_A0A096MXB6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6XGR9_F6XGR9_MACMU_9544 and tr_A0A0D9RJZ0_A0A0D9RJZ0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6XGR9_F6XGR9_MACMU_9544 and tr_A0A2K5KL36_A0A2K5KL36_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6XGR9_F6XGR9_MACMU_9544 and tr_A0A2K6E699_A0A2K6E699_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6XGR9_F6XGR9_MACMU_9544 and tr_A0A2K5YI00_A0A2K5YI00_MANLE_9568 are exactly identical! WARNING: Sequences tr_H9ETP9_H9ETP9_MACMU_9544 and tr_A0A2K5NET6_A0A2K5NET6_CERAT_9531 are exactly identical! WARNING: Sequences tr_I1PFL5_I1PFL5_ORYGL_4538 and tr_A0A0D3FP84_A0A0D3FP84_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_W2PU87_W2PU87_PHYPN_761204 and tr_W2KQD5_W2KQD5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A096NZG0_A0A096NZG0_PAPAN_9555 and tr_A0A2K6CRD6_A0A2K6CRD6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NZG0_A0A096NZG0_PAPAN_9555 and tr_A0A2K5YYK9_A0A2K5YYK9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3LQ52_A0A2I3LQ52_PAPAN_9555 and tr_A0A2K5P5B1_A0A2K5P5B1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091UNQ0_A0A091UNQ0_NIPNI_128390 and tr_A0A087R4J7_A0A087R4J7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0V1CPW4_A0A0V1CPW4_TRIBR_45882 and tr_A0A0V0TYF6_A0A0V0TYF6_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1L6D8_A0A0V1L6D8_9BILA_6335 and tr_A0A0V0ZNK8_A0A0V0ZNK8_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A124BYX0_A0A124BYX0_ASPNG_5061 and tr_A0A1L9NE81_A0A1L9NE81_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A226MNE3_A0A226MNE3_CALSU_9009 and tr_A0A226PQY9_A0A226PQY9_COLVI_9014 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/020621_run/phylogeny-snakemake/results/Q7Z2Y5/4_raxmlng_ancestral/Q7Z2Y5.raxml.reduced.phy Alignment comprises 1 partitions and 1582 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1582 Gaps: 49.32 % Invariant sites: 2.78 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z2Y5/4_raxmlng_ancestral/Q7Z2Y5.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/Q7Z2Y5/3_mltree/Q7Z2Y5.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 396 / 31680 [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: -395171.334478 [00:00:00 -395171.334478] Initial branch length optimization [00:00:04 -303871.499263] Model parameter optimization (eps = 0.100000) [00:02:18] Tree #1, final logLikelihood: -302953.620152 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.139930,0.225248) (0.086649,0.331720) (0.346612,0.589638) (0.426809,1.722929) 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/Q7Z2Y5/4_raxmlng_ancestral/Q7Z2Y5.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z2Y5/4_raxmlng_ancestral/Q7Z2Y5.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z2Y5/4_raxmlng_ancestral/Q7Z2Y5.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z2Y5/4_raxmlng_ancestral/Q7Z2Y5.raxml.log Analysis started: 03-Jun-2021 14:59:56 / finished: 03-Jun-2021 15:02:32 Elapsed time: 155.087 seconds Consumed energy: 10.463 Wh