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 22:45:38 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10071/2_msa/P10071_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10071/3_mltree/P10071.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10071/4_raxmlng_ancestral/P10071 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622663138
  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/P10071/2_msa/P10071_nogap_msa.fasta
[00:00:00] Loaded alignment with 994 taxa and 1580 sites

WARNING: Sequences tr_G3RYT4_G3RYT4_GORGO_9595 and tr_H2PWY4_H2PWY4_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RYT4_G3RYT4_GORGO_9595 and tr_A0A2I3RP19_A0A2I3RP19_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RYT4_G3RYT4_GORGO_9595 and tr_A0A2R9A8T3_A0A2R9A8T3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_E2R969_E2R969_CANLF_9615 and tr_A0A337RWA9_A0A337RWA9_FELCA_9685 are exactly identical!
WARNING: Sequences tr_H2R2A4_H2R2A4_PANTR_9598 and sp_Q9BZE0_GLIS2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R2A4_H2R2A4_PANTR_9598 and tr_A0A0D9RB62_A0A0D9RB62_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2R2A4_H2R2A4_PANTR_9598 and tr_A0A2K5NRS5_A0A2K5NRS5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2R2A4_H2R2A4_PANTR_9598 and tr_A0A2R9A0C5_A0A2R9A0C5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H0X5C4_H0X5C4_OTOGA_30611 and sp_O60481_ZIC3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F6RYU5_F6RYU5_MACMU_9544 and tr_A0A2K6BL12_A0A2K6BL12_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7Q1T9_G7Q1T9_MACFA_9541 and tr_A0A2I3NC06_A0A2I3NC06_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7Q1T9_G7Q1T9_MACFA_9541 and tr_A0A0D9R524_A0A0D9R524_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7Q1T9_G7Q1T9_MACFA_9541 and tr_A0A2K5MM50_A0A2K5MM50_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7Q1T9_G7Q1T9_MACFA_9541 and tr_A0A2K6DGL8_A0A2K6DGL8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7Q1T9_G7Q1T9_MACFA_9541 and tr_A0A2K5XCT1_A0A2K5XCT1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096N2D8_A0A096N2D8_PAPAN_9555 and tr_A0A2K5LFP4_A0A2K5LFP4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096N2D8_A0A096N2D8_PAPAN_9555 and tr_A0A2K5YY92_A0A2K5YY92_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3LU00_A0A2I3LU00_PAPAN_9555 and tr_A0A2K5KIW3_A0A2K5KIW3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A091EBN1_A0A091EBN1_CORBR_85066 and tr_A0A091GF80_A0A091GF80_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A1I7TNH1_A0A1I7TNH1_9PELO_1561998 and tr_A0A1I7TNH2_A0A1I7TNH2_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1D1UNB0_A0A1D1UNB0_RAMVA_947166 and tr_A0A1D1URF6_A0A1D1URF6_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A2D0SM80_A0A2D0SM80_ICTPU_7998 and tr_A0A2D0SM89_A0A2D0SM89_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SPW3_A0A2D0SPW3_ICTPU_7998 and tr_A0A2D0SQG1_A0A2D0SQG1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5MZH1_A0A2K5MZH1_CERAT_9531 and tr_A0A2K5ZWS0_A0A2K5ZWS0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K6C5P5_A0A2K6C5P5_MACNE_9545 and tr_A0A2K6A802_A0A2K6A802_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U3V869_A0A2U3V869_TURTR_9739 and tr_A0A2Y9LJX8_A0A2Y9LJX8_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U3V869_A0A2U3V869_TURTR_9739 and tr_A0A2Y9T350_A0A2Y9T350_PHYCD_9755 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/P10071/4_raxmlng_ancestral/P10071.raxml.reduced.phy

Alignment comprises 1 partitions and 1580 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 1580
Gaps: 56.93 %
Invariant sites: 0.00 %


NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10071/4_raxmlng_ancestral/P10071.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/P10071/3_mltree/P10071.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 395 / 31600
[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: -733810.692115

[00:00:00 -733810.692115] Initial branch length optimization
[00:00:07 -438404.058100] Model parameter optimization (eps = 0.100000)

[00:02:01] Tree #1, final logLikelihood: -437895.210947


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.057501,0.104965) (0.075592,0.310606) (0.363126,0.640311) (0.503781,1.464866) 
   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/P10071/4_raxmlng_ancestral/P10071.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10071/4_raxmlng_ancestral/P10071.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10071/4_raxmlng_ancestral/P10071.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10071/4_raxmlng_ancestral/P10071.raxml.log

Analysis started: 02-Jun-2021 22:45:38 / finished: 02-Jun-2021 22:47:53

Elapsed time: 134.999 seconds