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 04-Jun-2021 14:12:42 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P15529/2_msa/P15529_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P15529/3_mltree/P15529.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P15529/4_raxmlng_ancestral/P15529 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805162 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/P15529/2_msa/P15529_nogap_msa.fasta [00:00:00] Loaded alignment with 829 taxa and 392 sites WARNING: Sequences tr_M3YM36_M3YM36_MUSPF_9669 and tr_A0A2U3Y2V6_A0A2U3Y2V6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YM36_M3YM36_MUSPF_9669 and tr_A0A384BLL2_A0A384BLL2_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I2YBM4_A0A2I2YBM4_GORGO_9595 and tr_K6ZP09_K6ZP09_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YBM4_A0A2I2YBM4_GORGO_9595 and tr_F6XX70_F6XX70_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2YBM4_A0A2I2YBM4_GORGO_9595 and tr_A0A096NMJ8_A0A096NMJ8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2YBM4_A0A2I2YBM4_GORGO_9595 and tr_A0A0D9R1E0_A0A0D9R1E0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2YBM4_A0A2I2YBM4_GORGO_9595 and tr_A0A2K6DUX6_A0A2K6DUX6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2YBM4_A0A2I2YBM4_GORGO_9595 and tr_A0A2K6AK41_A0A2K6AK41_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2YBM4_A0A2I2YBM4_GORGO_9595 and tr_A0A2R9AR31_A0A2R9AR31_PANPA_9597 are exactly identical! WARNING: Sequences tr_F1PLW8_F1PLW8_CANLF_9615 and tr_A0A2U3VZ38_A0A2U3VZ38_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3SBS7_A0A2I3SBS7_PANTR_9598 and tr_A0A2R8ZDJ2_A0A2R8ZDJ2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q115_H2Q115_PANTR_9598 and tr_A0A2R8ZSE1_A0A2R8ZSE1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QWL4_H2QWL4_PANTR_9598 and sp_Q7Z407_CSMD3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QWL4_H2QWL4_PANTR_9598 and tr_A0A2R9C8Y9_A0A2R9C8Y9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2RBN8_H2RBN8_PANTR_9598 and tr_A0A2R9BSA1_A0A2R9BSA1_PANPA_9597 are exactly identical! WARNING: Sequences tr_I3MKQ0_I3MKQ0_ICTTR_43179 and tr_A0A3Q0DJI8_A0A3Q0DJI8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A2C9F1E0_A0A2C9F1E0_CAVPO_10141 and sp_P70105_MCP_CAVPO_10141 are exactly identical! WARNING: Sequences sp_Q6UXD5_SE6L2_HUMAN_9606 and tr_G7Q0V6_G7Q0V6_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5R240_A0A1D5R240_MACMU_9544 and tr_A0A0D9RF16_A0A0D9RF16_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5R240_A0A1D5R240_MACMU_9544 and tr_A0A2K6CPR3_A0A2K6CPR3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5R240_A0A1D5R240_MACMU_9544 and tr_A0A2K5Z8Z5_A0A2K5Z8Z5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7D9P8_F7D9P8_MACMU_9544 and tr_A0A2K6BKX3_A0A2K6BKX3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GSR2_F7GSR2_MACMU_9544 and tr_G8F4J7_G8F4J7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F1RSC6_F1RSC6_PIG_9823 and sp_P98110_LYAM2_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A096MUS6_A0A096MUS6_PAPAN_9555 and tr_A0A2K5ZIZ4_A0A2K5ZIZ4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096P0X0_A0A096P0X0_PAPAN_9555 and tr_A0A2K5M5G3_A0A2K5M5G3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1S3LH18_A0A1S3LH18_SALSA_8030 and tr_A0A060WHT8_A0A060WHT8_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2K5LCB9_A0A2K5LCB9_CERAT_9531 and tr_A0A2K6A0I5_A0A2K6A0I5_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 28 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/P15529/4_raxmlng_ancestral/P15529.raxml.reduced.phy Alignment comprises 1 partitions and 392 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 392 Gaps: 31.27 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P15529/4_raxmlng_ancestral/P15529.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/P15529/3_mltree/P15529.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 98 / 7840 [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: -187385.811617 [00:00:00 -187385.811617] Initial branch length optimization [00:00:01 -185585.811557] Model parameter optimization (eps = 0.100000) [00:00:28] Tree #1, final logLikelihood: -185068.916530 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.089807,0.177317) (0.060806,0.433534) (0.364592,0.822366) (0.484795,1.357041) 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/P15529/4_raxmlng_ancestral/P15529.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P15529/4_raxmlng_ancestral/P15529.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P15529/4_raxmlng_ancestral/P15529.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P15529/4_raxmlng_ancestral/P15529.raxml.log Analysis started: 04-Jun-2021 14:12:42 / finished: 04-Jun-2021 14:13:13 Elapsed time: 30.979 seconds