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 02-Jun-2021 15:10:08 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12830/2_msa/P12830_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12830/3_mltree/P12830.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12830/4_raxmlng_ancestral/P12830 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622635808 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_020621/phylogeny-snakemake/results/P12830/2_msa/P12830_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 882 sites WARNING: Sequences tr_G3R9R6_G3R9R6_GORGO_9595 and tr_H2PF89_H2PF89_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R9R6_G3R9R6_GORGO_9595 and tr_H2QQP7_H2QQP7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R9R6_G3R9R6_GORGO_9595 and sp_Q9Y6N8_CAD10_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TU99_A0A2I3TU99_PANTR_9598 and tr_A0A2R9BHQ4_A0A2R9BHQ4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8ND39_A0A2J8ND39_PANTR_9598 and sp_Q9ULB5_CADH7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8ND39_A0A2J8ND39_PANTR_9598 and tr_A0A2R9C879_A0A2R9C879_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R1Q6_H2R1Q6_PANTR_9598 and sp_P55285_CADH6_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R1Q6_H2R1Q6_PANTR_9598 and tr_A0A2R9AUM4_A0A2R9AUM4_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5NUS7_W5NUS7_SHEEP_9940 and tr_A2VDQ6_A2VDQ6_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F6WI86_F6WI86_MACMU_9544 and tr_A0A096N721_A0A096N721_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WI86_F6WI86_MACMU_9544 and tr_A0A2K6DZK2_A0A2K6DZK2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6ZW11_F6ZW11_MACMU_9544 and tr_G7PW74_G7PW74_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6ZW11_F6ZW11_MACMU_9544 and tr_A0A2K6ALU7_A0A2K6ALU7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DRD8_F7DRD8_MACMU_9544 and tr_G7P7A7_G7P7A7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DRD8_F7DRD8_MACMU_9544 and tr_A0A2K6DNF3_A0A2K6DNF3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FMS7_F7FMS7_MACMU_9544 and tr_A0A0D9RXE3_A0A0D9RXE3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7FMS7_F7FMS7_MACMU_9544 and tr_A0A2K5NBK4_A0A2K5NBK4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FMS7_F7FMS7_MACMU_9544 and tr_A0A2K6C316_A0A2K6C316_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FMS7_F7FMS7_MACMU_9544 and tr_A0A2K5ZBA0_A0A2K5ZBA0_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GFF0_F7GFF0_MACMU_9544 and tr_G7Q1A8_G7Q1A8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GFF0_F7GFF0_MACMU_9544 and tr_A0A096NJ47_A0A096NJ47_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GFF0_F7GFF0_MACMU_9544 and tr_A0A0D9QXB9_A0A0D9QXB9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GFF0_F7GFF0_MACMU_9544 and tr_A0A2K5M9M6_A0A2K5M9M6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GFF0_F7GFF0_MACMU_9544 and tr_A0A2K6E2P6_A0A2K6E2P6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GFF0_F7GFF0_MACMU_9544 and tr_A0A2K5YPU4_A0A2K5YPU4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HPS8_F7HPS8_MACMU_9544 and tr_G7P7A5_G7P7A5_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1L3U5_G1L3U5_AILME_9646 and tr_A0A384D1V4_A0A384D1V4_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7P7A9_G7P7A9_MACFA_9541 and tr_A0A2K6DIQ4_A0A2K6DIQ4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MLZ6_A0A096MLZ6_PAPAN_9555 and tr_A0A0D9RXC1_A0A0D9RXC1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MLZ6_A0A096MLZ6_PAPAN_9555 and tr_A0A2K5P2T0_A0A2K5P2T0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MLZ6_A0A096MLZ6_PAPAN_9555 and tr_A0A2K5Y6D7_A0A2K5Y6D7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NQS1_A0A096NQS1_PAPAN_9555 and tr_A0A2K5LC14_A0A2K5LC14_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MEP1_A0A2I3MEP1_PAPAN_9555 and tr_A0A2K5M0K6_A0A2K5M0K6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151N7C6_A0A151N7C6_ALLMI_8496 and tr_A0A1U7R317_A0A1U7R317_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A1U7TMA9_A0A1U7TMA9_TARSY_1868482 and tr_A0A2U4BDW2_A0A2U4BDW2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A1U7TMA9_A0A1U7TMA9_TARSY_1868482 and tr_A0A2Y9LX59_A0A2Y9LX59_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2K5N863_A0A2K5N863_CERAT_9531 and tr_A0A2K5Y2M1_A0A2K5Y2M1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4CMC1_A0A2U4CMC1_TURTR_9739 and tr_A0A2Y9P1F3_A0A2Y9P1F3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3W952_A0A2U3W952_ODORO_9708 and tr_A0A2U3YVD5_A0A2U3YVD5_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 39 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12830/4_raxmlng_ancestral/P12830.raxml.reduced.phy Alignment comprises 1 partitions and 882 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 882 Gaps: 16.77 % Invariant sites: 0.23 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12830/4_raxmlng_ancestral/P12830.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_020621/phylogeny-snakemake/results/P12830/3_mltree/P12830.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 221 / 17680 [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: -232846.021550 [00:00:00 -232846.021550] Initial branch length optimization [00:00:02 -232280.091202] Model parameter optimization (eps = 0.100000) [00:00:47] Tree #1, final logLikelihood: -231385.079997 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.182495,0.439044) (0.193149,0.463113) (0.356663,0.939502) (0.267693,1.850407) 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_020621/phylogeny-snakemake/results/P12830/4_raxmlng_ancestral/P12830.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12830/4_raxmlng_ancestral/P12830.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12830/4_raxmlng_ancestral/P12830.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12830/4_raxmlng_ancestral/P12830.raxml.log Analysis started: 02-Jun-2021 15:10:08 / finished: 02-Jun-2021 15:11:03 Elapsed time: 55.412 seconds