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 22:47:56 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07359/2_msa/P07359_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07359/3_mltree/P07359.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07359/4_raxmlng_ancestral/P07359 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622663276
  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/P07359/2_msa/P07359_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 652 sites

WARNING: Sequences tr_F1P4Y4_F1P4Y4_CHICK_9031 and tr_A0A091JMR2_A0A091JMR2_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_F1P4Y4_F1P4Y4_CHICK_9031 and tr_A0A091UTX7_A0A091UTX7_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_F1P4Y4_F1P4Y4_CHICK_9031 and tr_A0A087QL12_A0A087QL12_APTFO_9233 are exactly identical!
WARNING: Sequences tr_F1P4Y4_F1P4Y4_CHICK_9031 and tr_A0A091G5V9_A0A091G5V9_9AVES_55661 are exactly identical!
WARNING: Sequences tr_F1P4Y4_F1P4Y4_CHICK_9031 and tr_A0A0A0A9A4_A0A0A0A9A4_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_F1P4Y4_F1P4Y4_CHICK_9031 and tr_A0A2I0M3A6_A0A2I0M3A6_COLLI_8932 are exactly identical!
WARNING: Sequences tr_F1P4Y4_F1P4Y4_CHICK_9031 and tr_A0A093GSB4_A0A093GSB4_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_G3QNU0_G3QNU0_GORGO_9595 and sp_Q13641_TPBG_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PZZ8_H2PZZ8_PANTR_9598 and tr_A0A2R8ZGF9_A0A2R8ZGF9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QAB1_H2QAB1_PANTR_9598 and sp_P35858_ALS_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QY81_H2QY81_PANTR_9598 and tr_A0A2R8ZRC0_A0A2R8ZRC0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A158NHZ4_A0A158NHZ4_ATTCE_12957 and tr_A0A195BXM2_A0A195BXM2_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F7CT46_F7CT46_MACMU_9544 and tr_A0A2K6AWW0_A0A2K6AWW0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7FSB9_F7FSB9_MACMU_9544 and tr_G7NYR2_G7NYR2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7FSB9_F7FSB9_MACMU_9544 and tr_A0A0D9SC64_A0A0D9SC64_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7FSB9_F7FSB9_MACMU_9544 and tr_A0A2K5P8B1_A0A2K5P8B1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7FSB9_F7FSB9_MACMU_9544 and tr_A0A2K6CIU3_A0A2K6CIU3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7NTT7_G7NTT7_MACFA_9541 and tr_A0A2K6B798_A0A2K6B798_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NDP7_A0A096NDP7_PAPAN_9555 and tr_A0A0D9SAC3_A0A0D9SAC3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096NDP7_A0A096NDP7_PAPAN_9555 and tr_A0A2K5L1R7_A0A2K5L1R7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NDP7_A0A096NDP7_PAPAN_9555 and tr_A0A2K5X9U0_A0A2K5X9U0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096NR13_A0A096NR13_PAPAN_9555 and tr_A0A2K5KXE2_A0A2K5KXE2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A091E8N6_A0A091E8N6_CORBR_85066 and tr_A0A091VUJ5_A0A091VUJ5_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A0V1DDJ5_A0A0V1DDJ5_TRIBR_45882 and tr_A0A0V0X7B4_A0A0V0X7B4_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1DDJ5_A0A0V1DDJ5_TRIBR_45882 and tr_A0A0V1LTV1_A0A0V1LTV1_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1DDJ5_A0A0V1DDJ5_TRIBR_45882 and tr_A0A0V1PFC3_A0A0V1PFC3_9BILA_92180 are exactly identical!
WARNING: Duplicate sequences found: 26

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/P07359/4_raxmlng_ancestral/P07359.raxml.reduced.phy

Alignment comprises 1 partitions and 652 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 652
Gaps: 52.08 %
Invariant sites: 0.15 %


NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07359/4_raxmlng_ancestral/P07359.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/P07359/3_mltree/P07359.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: -268095.842329

[00:00:00 -268095.842329] Initial branch length optimization
[00:00:01 -266095.087818] Model parameter optimization (eps = 0.100000)

[00:01:05] Tree #1, final logLikelihood: -263700.298774


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.077854,0.350970) (0.074365,0.330377) (0.409313,0.992624) (0.438468,1.235694) 
   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/P07359/4_raxmlng_ancestral/P07359.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07359/4_raxmlng_ancestral/P07359.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07359/4_raxmlng_ancestral/P07359.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07359/4_raxmlng_ancestral/P07359.raxml.log

Analysis started: 02-Jun-2021 22:47:56 / finished: 02-Jun-2021 22:49:08

Elapsed time: 71.670 seconds