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 19-Jul-2021 13:08:32 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95834/2_msa/O95834_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95834/3_mltree/O95834.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95834/4_raxmlng_ancestral/O95834 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626689312
  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_300621/phylogeny-snakemake/results/O95834/2_msa/O95834_nogap_msa.fasta
[00:00:00] Loaded alignment with 957 taxa and 649 sites

WARNING: Fully undetermined sequences found: 10

WARNING: Sequences tr_B4QKG9_B4QKG9_DROSI_7240 and tr_B4HHU6_B4HHU6_DROSE_7238 are exactly identical!
WARNING: Sequences tr_M3YBT7_M3YBT7_MUSPF_9669 and tr_A0A2Y9KSZ2_A0A2Y9KSZ2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YGK8_M3YGK8_MUSPF_9669 and tr_A0A337SQZ4_A0A337SQZ4_FELCA_9685 are exactly identical!
WARNING: Sequences tr_B6QM56_B6QM56_TALMQ_441960 and tr_A0A093XKW6_A0A093XKW6_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_H2RDN8_H2RDN8_PANTR_9598 and sp_Q32P44_EMAL3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F6RYA9_F6RYA9_MACMU_9544 and tr_A0A2I3N287_A0A2I3N287_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6RYA9_F6RYA9_MACMU_9544 and tr_A0A2K5LNH6_A0A2K5LNH6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7GAG9_F7GAG9_MACMU_9544 and tr_A0A2K6BZ55_A0A2K6BZ55_MACNE_9545 are exactly identical!
WARNING: Sequences tr_B3SCP1_B3SCP1_TRIAD_10228 and tr_A0A369RZI6_A0A369RZI6_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G7PB51_G7PB51_MACFA_9541 and tr_A0A2K5ZTR0_A0A2K5ZTR0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096MVX9_A0A096MVX9_PAPAN_9555 and tr_A0A2K5NN62_A0A2K5NN62_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096MVX9_A0A096MVX9_PAPAN_9555 and tr_A0A2K5ZY08_A0A2K5ZY08_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096N6R7_A0A096N6R7_PAPAN_9555 and tr_A0A2K5NGN7_A0A2K5NGN7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0D9RN45_A0A0D9RN45_CHLSB_60711 and tr_A0A2K5YL53_A0A2K5YL53_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0W8CQF8_A0A0W8CQF8_PHYNI_4790 and tr_W2I3Y1_W2I3Y1_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A2D0QPY8_A0A2D0QPY8_ICTPU_7998 and tr_W6AC67_W6AC67_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0R9P9_A0A2D0R9P9_ICTPU_7998 and tr_A0A2D0RB10_A0A2D0RB10_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0R9Q3_A0A2D0R9Q3_ICTPU_7998 and tr_A0A2D0RBQ5_A0A2D0RBQ5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RN96_A0A2D0RN96_ICTPU_7998 and tr_A0A2D0RNA5_A0A2D0RNA5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RN96_A0A2D0RN96_ICTPU_7998 and tr_A0A2D0RP98_A0A2D0RP98_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RNA6_A0A2D0RNA6_ICTPU_7998 and tr_A0A2D0RPV8_A0A2D0RPV8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RSF9_A0A2D0RSF9_ICTPU_7998 and tr_A0A2D0RSG1_A0A2D0RSG1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RSF9_A0A2D0RSF9_ICTPU_7998 and tr_A0A2D0RSG3_A0A2D0RSG3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RSF9_A0A2D0RSF9_ICTPU_7998 and tr_A0A2D0RU04_A0A2D0RU04_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2Y9NDZ3_A0A2Y9NDZ3_DELLE_9749 and tr_A0A383YWV8_A0A383YWV8_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 25

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95834/4_raxmlng_ancestral/O95834.raxml.reduced.phy

Alignment comprises 1 partitions and 649 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 649
Gaps: 17.69 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95834/4_raxmlng_ancestral/O95834.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_300621/phylogeny-snakemake/results/O95834/3_mltree/O95834.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 163 / 13040
[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: -240227.188639

[00:00:00 -240227.188639] Initial branch length optimization
[00:00:01 -237188.136248] Model parameter optimization (eps = 0.100000)

[00:00:57] Tree #1, final logLikelihood: -235478.801175


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.185982,0.878931) (0.193601,0.783460) (0.434579,0.910261) (0.185839,1.556598) 
   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_300621/phylogeny-snakemake/results/O95834/4_raxmlng_ancestral/O95834.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95834/4_raxmlng_ancestral/O95834.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95834/4_raxmlng_ancestral/O95834.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95834/4_raxmlng_ancestral/O95834.raxml.log

Analysis started: 19-Jul-2021 13:08:32 / finished: 19-Jul-2021 13:09:35

Elapsed time: 62.808 seconds