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 17-Jul-2021 08:10:17 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/2_msa/A0A075B6I1_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/3_mltree/A0A075B6I1.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/4_raxmlng_ancestral/A0A075B6I1 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626498617
  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/A0A075B6I1/2_msa/A0A075B6I1_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 120 sites

WARNING: Sequences tr_A0A2I2YJC5_A0A2I2YJC5_GORGO_9595 and tr_A0A2I3RV96_A0A2I3RV96_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YMS6_A0A2I2YMS6_GORGO_9595 and tr_A0A2R9AK91_A0A2R9AK91_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RK08_G3RK08_GORGO_9595 and tr_A0A2I3S3B0_A0A2I3S3B0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RK08_G3RK08_GORGO_9595 and sp_P12018_VPREB_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RK08_G3RK08_GORGO_9595 and tr_A0A2R9BNT9_A0A2R9BNT9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_J9P8P3_J9P8P3_CANLF_9615 and tr_J9PAD4_J9PAD4_CANLF_9615 are exactly identical!
WARNING: Sequences tr_A0A2I3RYP8_A0A2I3RYP8_PANTR_9598 and tr_A0A2R9AL33_A0A2R9AL33_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SR69_A0A2I3SR69_PANTR_9598 and tr_A0A2R8ZB48_A0A2R8ZB48_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SXH8_A0A2I3SXH8_PANTR_9598 and tr_A0A2R9AKM0_A0A2R9AKM0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3T0N1_A0A2I3T0N1_PANTR_9598 and tr_A0A2R8ZDA9_A0A2R8ZDA9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TAX1_A0A2I3TAX1_PANTR_9598 and tr_A0A2R9AKE1_A0A2R9AKE1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TQF9_A0A2I3TQF9_PANTR_9598 and tr_A0A2R8ZQY1_A0A2R8ZQY1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TUR2_A0A2I3TUR2_PANTR_9598 and tr_A0A2R8ZX92_A0A2R8ZX92_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H0XVL7_H0XVL7_OTOGA_30611 and tr_H0Y0H4_H0Y0H4_OTOGA_30611 are exactly identical!
WARNING: Sequences sp_A0A0B4J1Y8_LV949_HUMAN_9606 and tr_A0A2R9A2R6_A0A2R9A2R6_PANPA_9597 are exactly identical!
WARNING: Sequences sp_A0A0B4J2D9_KVD13_HUMAN_9606 and sp_P0DP09_KV113_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_P01593_KVD33_HUMAN_9606 and sp_P01594_KV133_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A1D5QR47_A0A1D5QR47_MACMU_9544 and tr_G8F2W8_G8F2W8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7F215_F7F215_MACMU_9544 and tr_A0A2K6ARQ7_A0A2K6ARQ7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PHB9_G7PHB9_MACFA_9541 and tr_A0A096NSB1_A0A096NSB1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PHB9_G7PHB9_MACFA_9541 and tr_A0A2K5XPA3_A0A2K5XPA3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3LZC8_A0A2I3LZC8_PAPAN_9555 and tr_A0A2K6B468_A0A2K6B468_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3LZC8_A0A2I3LZC8_PAPAN_9555 and tr_A0A2K5XFL9_A0A2K5XFL9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3N776_A0A2I3N776_PAPAN_9555 and tr_A0A2K5NT28_A0A2K5NT28_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3N776_A0A2I3N776_PAPAN_9555 and tr_A0A2K6ALR0_A0A2K6ALR0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0D9RN59_A0A0D9RN59_CHLSB_60711 and tr_A0A0D9RN85_A0A0D9RN85_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2K5KMJ7_A0A2K5KMJ7_CERAT_9531 and tr_A0A2K5XYB4_A0A2K5XYB4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5NTZ8_A0A2K5NTZ8_CERAT_9531 and tr_A0A2K6CXY6_A0A2K6CXY6_MACNE_9545 are exactly identical!
WARNING: Duplicate sequences found: 28

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/A0A075B6I1/4_raxmlng_ancestral/A0A075B6I1.raxml.reduced.phy

Alignment comprises 1 partitions and 120 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 120
Gaps: 11.54 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/4_raxmlng_ancestral/A0A075B6I1.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/A0A075B6I1/3_mltree/A0A075B6I1.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 30 / 2400
[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: -55802.023178

[00:00:00 -55802.023178] Initial branch length optimization
[00:00:00 -55493.505465] Model parameter optimization (eps = 0.100000)

[00:00:15] Tree #1, final logLikelihood: -55175.144388


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.241619,0.464763) (0.124628,0.546279) (0.508006,0.939250) (0.125748,2.723530) 
   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/A0A075B6I1/4_raxmlng_ancestral/A0A075B6I1.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/4_raxmlng_ancestral/A0A075B6I1.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/4_raxmlng_ancestral/A0A075B6I1.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/4_raxmlng_ancestral/A0A075B6I1.raxml.log

Analysis started: 17-Jul-2021 08:10:17 / finished: 17-Jul-2021 08:10:34

Elapsed time: 16.577 seconds