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 22:50:27 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UHD2/2_msa/Q9UHD2_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UHD2/3_mltree/Q9UHD2.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UHD2/4_raxmlng_ancestral/Q9UHD2 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622663427
  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/Q9UHD2/2_msa/Q9UHD2_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 729 sites

WARNING: Sequences tr_M3XV05_M3XV05_MUSPF_9669 and tr_A0A2Y9KTH4_A0A2Y9KTH4_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I2Z864_A0A2I2Z864_GORGO_9595 and sp_Q8IYT8_ULK2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QFX0_G3QFX0_GORGO_9595 and sp_Q96NX5_KCC1G_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QFX0_G3QFX0_GORGO_9595 and tr_A0A2R9CCR5_A0A2R9CCR5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RVG0_G3RVG0_GORGO_9595 and tr_K7C5W4_K7C5W4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RVG0_G3RVG0_GORGO_9595 and sp_Q14164_IKKE_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q6E2_H2Q6E2_PANTR_9598 and tr_A0A2R8ZIM2_A0A2R8ZIM2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A088APZ5_A0A088APZ5_APIME_7460 and tr_A0A2A3EIA7_A0A2A3EIA7_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NF46_A0A158NF46_ATTCE_12957 and tr_A0A195AVD0_A0A195AVD0_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NI20_A0A158NI20_ATTCE_12957 and tr_A0A151I4C2_A0A151I4C2_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F7DBZ3_F7DBZ3_MACMU_9544 and tr_A0A096MZ73_A0A096MZ73_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7DBZ3_F7DBZ3_MACMU_9544 and tr_A0A2K6DYC3_A0A2K6DYC3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7DBZ3_F7DBZ3_MACMU_9544 and tr_A0A2K5Z5D5_A0A2K5Z5D5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7MEP2_G7MEP2_MACMU_9544 and tr_G7NUP1_G7NUP1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7MEP2_G7MEP2_MACMU_9544 and tr_A0A0D9RRT3_A0A0D9RRT3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7MEP2_G7MEP2_MACMU_9544 and tr_A0A2K6BLD4_A0A2K6BLD4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H9EV28_H9EV28_MACMU_9544 and tr_A0A096P352_A0A096P352_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F4WEJ1_F4WEJ1_ACREC_103372 and tr_A0A195FL43_A0A195FL43_9HYME_34720 are exactly identical!
WARNING: Sequences tr_W2QJE2_W2QJE2_PHYPN_761204 and tr_W2LN77_W2LN77_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2RJX7_W2RJX7_PHYPN_761204 and tr_A0A0W8D448_A0A0W8D448_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A3B6B6T5_A0A3B6B6T5_WHEAT_4565 and tr_A0A3B6CEA6_A0A3B6CEA6_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A096NAP5_A0A096NAP5_PAPAN_9555 and tr_A0A2K5N4K8_A0A2K5N4K8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NAP5_A0A096NAP5_PAPAN_9555 and tr_A0A2K6AA90_A0A2K6AA90_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0D2T6G9_A0A0D2T6G9_GOSRA_29730 and tr_A0A1U8NA08_A0A1U8NA08_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0A1NFY1_A0A0A1NFY1_9FUNG_58291 and tr_A0A367JJQ4_A0A367JJQ4_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0A1P849_A0A0A1P849_9FUNG_58291 and tr_A0A367K7D6_A0A367K7D6_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0V0ZD19_A0A0V0ZD19_9BILA_990121 and tr_A0A0V0ZED4_A0A0V0ZED4_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A226MH32_A0A226MH32_CALSU_9009 and tr_A0A226PWN5_A0A226PWN5_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0SKI3_A0A2D0SKI3_ICTPU_7998 and tr_A0A2D0SKI6_A0A2D0SKI6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2I1G350_A0A2I1G350_9GLOM_588596 and tr_A0A2H5SM59_A0A2H5SM59_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2U4CAT5_A0A2U4CAT5_TURTR_9739 and tr_A0A384AWY4_A0A384AWY4_BALAS_310752 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/Q9UHD2/4_raxmlng_ancestral/Q9UHD2.raxml.reduced.phy

Alignment comprises 1 partitions and 729 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 729
Gaps: 36.31 %
Invariant sites: 0.14 %


NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UHD2/4_raxmlng_ancestral/Q9UHD2.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/Q9UHD2/3_mltree/Q9UHD2.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 183 / 14640
[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: -311657.514242

[00:00:00 -311657.514242] Initial branch length optimization
[00:00:02 -310575.454115] Model parameter optimization (eps = 0.100000)

[00:00:59] Tree #1, final logLikelihood: -309550.769529


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.080098,0.273062) (0.114224,0.302654) (0.395643,0.830166) (0.410035,1.500137) 
   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/Q9UHD2/4_raxmlng_ancestral/Q9UHD2.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UHD2/4_raxmlng_ancestral/Q9UHD2.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UHD2/4_raxmlng_ancestral/Q9UHD2.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UHD2/4_raxmlng_ancestral/Q9UHD2.raxml.log

Analysis started: 02-Jun-2021 22:50:27 / finished: 02-Jun-2021 22:51:33

Elapsed time: 65.640 seconds