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 13:38:24 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08AG5/2_msa/Q08AG5_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08AG5/3_mltree/Q08AG5.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08AG5/4_raxmlng_ancestral/Q08AG5 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803104 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/Q08AG5/2_msa/Q08AG5_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 666 sites WARNING: Sequences tr_A2ARR6_A2ARR6_MOUSE_10090 and tr_A2AW66_A2AW66_MOUSE_10090 are exactly identical! WARNING: Sequences tr_G3QSA3_G3QSA3_GORGO_9595 and tr_H2QFF2_H2QFF2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QSA3_G3QSA3_GORGO_9595 and tr_A0A2R8ZEJ9_A0A2R8ZEJ9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SCR4_G3SCR4_GORGO_9595 and sp_Q7L945_ZN627_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RPA8_A0A2I3RPA8_PANTR_9598 and tr_A0A2R8ZXM8_A0A2R8ZXM8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3S2B0_A0A2I3S2B0_PANTR_9598 and tr_A0A2R9BB51_A0A2R9BB51_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3T2W7_A0A2I3T2W7_PANTR_9598 and sp_Q9ULM2_ZN490_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q1G5_H2Q1G5_PANTR_9598 and sp_Q15973_ZN124_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q1G5_H2Q1G5_PANTR_9598 and tr_A0A2R9ATA1_A0A2R9ATA1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QFV8_H2QFV8_PANTR_9598 and tr_A0A2R9A264_A0A2R9A264_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R1T8_H2R1T8_PANTR_9598 and sp_Q8TBZ8_ZN564_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7D7J1_K7D7J1_PANTR_9598 and tr_A0A2R9APT9_A0A2R9APT9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6UPX1_F6UPX1_MACMU_9544 and tr_A0A2K5N4G8_A0A2K5N4G8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6UPX1_F6UPX1_MACMU_9544 and tr_A0A2K6D4D0_A0A2K6D4D0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7CT89_F7CT89_MACMU_9544 and tr_A0A2K6CV10_A0A2K6CV10_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GDG2_F7GDG2_MACMU_9544 and tr_A0A096MVU8_A0A096MVU8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GDG2_F7GDG2_MACMU_9544 and tr_A0A0D9S896_A0A0D9S896_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GDG2_F7GDG2_MACMU_9544 and tr_A0A2K5LPR7_A0A2K5LPR7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GDG2_F7GDG2_MACMU_9544 and tr_A0A2K6BKJ1_A0A2K6BKJ1_MACNE_9545 are exactly identical! WARNING: Sequences tr_H9ERQ6_H9ERQ6_MACMU_9544 and tr_G7PYR0_G7PYR0_MACFA_9541 are exactly identical! WARNING: Sequences tr_H9ERQ6_H9ERQ6_MACMU_9544 and tr_A0A2K6D8Q9_A0A2K6D8Q9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PZ52_G7PZ52_MACFA_9541 and tr_A0A2K6D4T1_A0A2K6D4T1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PZG7_G7PZG7_MACFA_9541 and tr_A0A2K6A5E0_A0A2K6A5E0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MU12_A0A0A0MU12_PAPAN_9555 and tr_A0A2K5ZCG0_A0A2K5ZCG0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MWC0_A0A0A0MWC0_PAPAN_9555 and tr_A0A2K5LT78_A0A2K5LT78_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0A0MWC0_A0A0A0MWC0_PAPAN_9555 and tr_A0A2K5ZDE5_A0A2K5ZDE5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3M705_A0A2I3M705_PAPAN_9555 and tr_A0A2K5ME88_A0A2K5ME88_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3NGA2_A0A2I3NGA2_PAPAN_9555 and tr_A0A0D9S5G7_A0A0D9S5G7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2K5LA58_A0A2K5LA58_CERAT_9531 and tr_A0A2K5YPZ4_A0A2K5YPZ4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5LPU1_A0A2K5LPU1_CERAT_9531 and tr_A0A2K6A833_A0A2K6A833_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5MY98_A0A2K5MY98_CERAT_9531 and tr_A0A2K5ZTE5_A0A2K5ZTE5_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 31 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/Q08AG5/4_raxmlng_ancestral/Q08AG5.raxml.reduced.phy Alignment comprises 1 partitions and 666 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 666 Gaps: 34.11 % Invariant sites: 7.51 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08AG5/4_raxmlng_ancestral/Q08AG5.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/Q08AG5/3_mltree/Q08AG5.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 167 / 13360 [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: -240375.414402 [00:00:00 -240375.414402] Initial branch length optimization [00:00:01 -240080.756820] Model parameter optimization (eps = 0.100000) [00:00:48] Tree #1, final logLikelihood: -239125.536140 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.129083,0.195707) (0.123661,0.638053) (0.437041,0.957596) (0.310215,1.538695) 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/Q08AG5/4_raxmlng_ancestral/Q08AG5.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08AG5/4_raxmlng_ancestral/Q08AG5.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08AG5/4_raxmlng_ancestral/Q08AG5.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08AG5/4_raxmlng_ancestral/Q08AG5.raxml.log Analysis started: 04-Jun-2021 13:38:24 / finished: 04-Jun-2021 13:39:18 Elapsed time: 54.596 seconds