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 23:46:27 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07477/2_msa/P07477_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07477/3_mltree/P07477.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07477/4_raxmlng_ancestral/P07477 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622666787 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/P07477/2_msa/P07477_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 247 sites WARNING: Sequences tr_G3QGF3_G3QGF3_GORGO_9595 and tr_H2RDY5_H2RDY5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QGF3_G3QGF3_GORGO_9595 and sp_Q9UKQ9_KLK9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QGF3_G3QGF3_GORGO_9595 and tr_A0A2R9BKN4_A0A2R9BKN4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3RV51_A0A2I3RV51_PANTR_9598 and tr_A0A2R9BIK0_A0A2R9BIK0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3T1E2_A0A2I3T1E2_PANTR_9598 and tr_A0A2R9BGV3_A0A2R9BGV3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3T245_A0A2I3T245_PANTR_9598 and tr_A0A2R9B8I7_A0A2R9B8I7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QGY8_H2QGY8_PANTR_9598 and tr_A0A2R9BX10_A0A2R9BX10_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QGZ2_H2QGZ2_PANTR_9598 and sp_O60259_KLK8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QGZ2_H2QGZ2_PANTR_9598 and tr_A0A2R9BP14_A0A2R9BP14_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QGZ3_H2QGZ3_PANTR_9598 and tr_A0A2R9CLY3_A0A2R9CLY3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QGZ4_H2QGZ4_PANTR_9598 and sp_Q9UKR3_KLK13_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q92876_KLK6_HUMAN_9606 and tr_A0A2R8ZUX5_A0A2R8ZUX5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QDH0_A0A1D5QDH0_MACMU_9544 and tr_A0A2K5YUD6_A0A2K5YUD6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6QBI7_F6QBI7_MACMU_9544 and tr_G7PYG4_G7PYG4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6QBI7_F6QBI7_MACMU_9544 and tr_A0A2K6CXK2_A0A2K6CXK2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6QBV6_F6QBV6_MACMU_9544 and tr_A0A2I3LCP7_A0A2I3LCP7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6QBV6_F6QBV6_MACMU_9544 and tr_A0A2K5M158_A0A2K5M158_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6V9H9_F6V9H9_MACMU_9544 and tr_A0A0A0MXD1_A0A0A0MXD1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6V9H9_F6V9H9_MACMU_9544 and tr_A0A2K6AD31_A0A2K6AD31_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6X1T9_F6X1T9_MACMU_9544 and tr_A0A2K6EAW7_A0A2K6EAW7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6XIP4_F6XIP4_MACMU_9544 and tr_G7PYG1_G7PYG1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1B8XYX9_A0A1B8XYX9_XENTR_8364 and tr_L7N308_L7N308_XENTR_8364 are exactly identical! WARNING: Sequences tr_F6UWG2_F6UWG2_CIOIN_7719 and tr_F6WT44_F6WT44_CIOIN_7719 are exactly identical! WARNING: Sequences tr_G7PYF6_G7PYF6_MACFA_9541 and tr_A0A0D9S529_A0A0D9S529_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PYF6_G7PYF6_MACFA_9541 and tr_A0A2K6E551_A0A2K6E551_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PYG3_G7PYG3_MACFA_9541 and tr_A0A2K6BIL5_A0A2K6BIL5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PYG7_G7PYG7_MACFA_9541 and tr_A0A2K6E7D9_A0A2K6E7D9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D9S542_A0A0D9S542_CHLSB_60711 and tr_A0A2K5M7V2_A0A2K5M7V2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9S542_A0A0D9S542_CHLSB_60711 and tr_A0A2K5YQT5_A0A2K5YQT5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1S2X2M3_A0A1S2X2M3_SALSA_8030 and sp_P35031_TRY1_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3RXS2_A0A1S3RXS2_SALSA_8030 and tr_B5X8S0_B5X8S0_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A2K5MIW8_A0A2K5MIW8_CERAT_9531 and tr_A0A2K5Y9Q1_A0A2K5Y9Q1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5NC84_A0A2K5NC84_CERAT_9531 and tr_A0A2K5YYS0_A0A2K5YYS0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5NL70_A0A2K5NL70_CERAT_9531 and tr_A0A2K5YLA9_A0A2K5YLA9_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 34 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/P07477/4_raxmlng_ancestral/P07477.raxml.reduced.phy Alignment comprises 1 partitions and 247 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 247 Gaps: 6.01 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07477/4_raxmlng_ancestral/P07477.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/P07477/3_mltree/P07477.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 62 / 4960 [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: -125464.641997 [00:00:00 -125464.641997] Initial branch length optimization [00:00:00 -125191.477048] Model parameter optimization (eps = 0.100000) [00:00:23] Tree #1, final logLikelihood: -124860.224258 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.246539,0.365630) (0.195711,0.417990) (0.315427,1.099275) (0.242323,1.986239) 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/P07477/4_raxmlng_ancestral/P07477.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07477/4_raxmlng_ancestral/P07477.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07477/4_raxmlng_ancestral/P07477.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07477/4_raxmlng_ancestral/P07477.raxml.log Analysis started: 02-Jun-2021 23:46:27 / finished: 02-Jun-2021 23:46:53 Elapsed time: 25.365 seconds