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 13:53:51 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15067/2_msa/Q15067_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15067/3_mltree/Q15067.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15067/4_raxmlng_ancestral/Q15067 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622804031
  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/Q15067/2_msa/Q15067_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 660 sites

WARNING: Sequences tr_J3K9M2_J3K9M2_COCIM_246410 and tr_E9CRI6_E9CRI6_COCPS_443226 are exactly identical!
WARNING: Sequences tr_B8MXD8_B8MXD8_ASPFN_332952 and tr_Q2USC8_Q2USC8_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8MXD8_B8MXD8_ASPFN_332952 and tr_A0A1S9DVY1_A0A1S9DVY1_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UFR0_A0A179UFR0_BLAGS_559298 and tr_C5GFL4_C5GFL4_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_A0A2I3T025_A0A2I3T025_PANTR_9598 and tr_A0A2R9BBX9_A0A2R9BBX9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FW12_F9FW12_FUSOF_660025 and tr_A0A0D2XIX9_A0A0D2XIX9_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FW12_F9FW12_FUSOF_660025 and tr_X0BBT2_X0BBT2_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FW12_F9FW12_FUSOF_660025 and tr_A0A2H3TEY2_A0A2H3TEY2_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FW12_F9FW12_FUSOF_660025 and tr_A0A2H3HRA5_A0A2H3HRA5_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_C6H2G1_C6H2G1_AJECH_544712 and tr_F0U560_F0U560_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A0E0HJK4_A0A0E0HJK4_ORYNI_4536 and tr_A2Y8A0_A2Y8A0_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0HJK4_A0A0E0HJK4_ORYNI_4536 and tr_A0A0E0DVF4_A0A0E0DVF4_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0HJK4_A0A0E0HJK4_ORYNI_4536 and tr_A0A0E0A3U2_A0A0E0A3U2_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_G7XZB4_G7XZB4_ASPKW_1033177 and tr_A0A146EZR6_A0A146EZR6_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A0A0E0PSD1_A0A0E0PSD1_ORYRU_4529 and tr_Q8H631_Q8H631_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_W2RHA1_W2RHA1_PHYPN_761204 and tr_A0A0W8BWN2_A0A0W8BWN2_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2RHA5_W2RHA5_PHYPN_761204 and tr_A0A0W8CAL6_A0A0W8CAL6_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2RHA5_W2RHA5_PHYPN_761204 and tr_W2JWZ4_W2JWZ4_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015KAT2_A0A015KAT2_9GLOM_1432141 and tr_A0A2I1G402_A0A2I1G402_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015KAT2_A0A015KAT2_9GLOM_1432141 and tr_U9TY99_U9TY99_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0A1N6T4_A0A0A1N6T4_9FUNG_58291 and tr_A0A367JKT3_A0A367JKT3_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A100IFN0_A0A100IFN0_ASPNG_5061 and tr_A0A1L9MXA6_A0A1L9MXA6_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1S4BUI2_A0A1S4BUI2_TOBAC_4097 and tr_A0A1U7X3Q7_A0A1U7X3Q7_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1Y1VWH8_A0A1Y1VWH8_9FUNG_1314790 and tr_A0A1Y1Z0Q9_A0A1Y1Z0Q9_9FUNG_1314790 are exactly identical!
WARNING: Sequences tr_A0A2K5KZ57_A0A2K5KZ57_CERAT_9531 and tr_A0A2K5XRH3_A0A2K5XRH3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5MXA9_A0A2K5MXA9_CERAT_9531 and tr_A0A2K6C0N1_A0A2K6C0N1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2G4SFP8_A0A2G4SFP8_9FUNG_1340429 and tr_A0A367K8V3_A0A367K8V3_9FUNG_86630 are exactly identical!
WARNING: Duplicate sequences found: 27

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/Q15067/4_raxmlng_ancestral/Q15067.raxml.reduced.phy

Alignment comprises 1 partitions and 660 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 660
Gaps: 6.34 %
Invariant sites: 0.76 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15067/4_raxmlng_ancestral/Q15067.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/Q15067/3_mltree/Q15067.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 165 / 13200
[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: -353022.576071

[00:00:00 -353022.576071] Initial branch length optimization
[00:00:01 -352814.684939] Model parameter optimization (eps = 0.100000)

[00:00:31] Tree #1, final logLikelihood: -351886.568002


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.166642,0.371916) (0.277397,0.470851) (0.326395,1.016713) (0.229566,2.071564) 
   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/Q15067/4_raxmlng_ancestral/Q15067.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15067/4_raxmlng_ancestral/Q15067.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15067/4_raxmlng_ancestral/Q15067.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15067/4_raxmlng_ancestral/Q15067.raxml.log

Analysis started: 04-Jun-2021 13:53:51 / finished: 04-Jun-2021 13:54:29

Elapsed time: 37.684 seconds