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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 03-Jun-2021 03:26:32 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00451/2_msa/P00451_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00451/3_mltree/P00451.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00451/4_raxmlng_ancestral/P00451 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622679992
  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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00451/2_msa/P00451_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 2351 sites

WARNING: Sequences tr_M3Y3H4_M3Y3H4_MUSPF_9669 and tr_A0A2Y9KE16_A0A2Y9KE16_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Y9I9_M3Y9I9_MUSPF_9669 and tr_A0A2U3XS10_A0A2U3XS10_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3Y9I9_M3Y9I9_MUSPF_9669 and tr_A0A2Y9JHM6_A0A2Y9JHM6_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I2Y2T5_A0A2I2Y2T5_GORGO_9595 and tr_H2PG16_H2PG16_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2Y2T5_A0A2I2Y2T5_GORGO_9595 and tr_A0A2I3T8Y9_A0A2I3T8Y9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R279_G3R279_GORGO_9595 and sp_O60462_NRP2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2J8L658_A0A2J8L658_PANTR_9598 and tr_A0A2R8ZY45_A0A2R8ZY45_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q1T2_H2Q1T2_PANTR_9598 and tr_A0A2R8Z9X4_A0A2R8Z9X4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QNJ9_H2QNJ9_PANTR_9598 and tr_A0A2R9AYC2_A0A2R9AYC2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7G9W1_F7G9W1_MACMU_9544 and tr_G7PL91_G7PL91_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7G9W1_F7G9W1_MACMU_9544 and tr_A0A096N6G9_A0A096N6G9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7G9W1_F7G9W1_MACMU_9544 and tr_A0A2K6D5X4_A0A2K6D5X4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7G9W1_F7G9W1_MACMU_9544 and tr_A0A2K5Z5G7_A0A2K5Z5G7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7HHM6_F7HHM6_MACMU_9544 and tr_G7PEQ1_G7PEQ1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7MYS0_G7MYS0_MACMU_9544 and tr_G7P9E2_G7P9E2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A096MMM3_A0A096MMM3_PAPAN_9555 and tr_A0A0D9RQQ2_A0A0D9RQQ2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096MMM3_A0A096MMM3_PAPAN_9555 and tr_A0A2K6DVL4_A0A2K6DVL4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096MMM3_A0A096MMM3_PAPAN_9555 and tr_A0A2K5YLW5_A0A2K5YLW5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096P459_A0A096P459_PAPAN_9555 and tr_A0A2K5N9G1_A0A2K5N9G1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096P459_A0A096P459_PAPAN_9555 and tr_A0A2K6AFS3_A0A2K6AFS3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2D0PSJ7_A0A2D0PSJ7_ICTPU_7998 and tr_W5UIZ7_W5UIZ7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T7K4_A0A2D0T7K4_ICTPU_7998 and tr_W5UAK2_W5UAK2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4AWH0_A0A2U4AWH0_TURTR_9739 and tr_A0A2Y9FUA6_A0A2Y9FUA6_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U4BN37_A0A2U4BN37_TURTR_9739 and tr_A0A2U4BNF8_A0A2U4BNF8_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2U4BN42_A0A2U4BN42_TURTR_9739 and tr_A0A2U4BN43_A0A2U4BN43_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2U4BN42_A0A2U4BN42_TURTR_9739 and tr_A0A2U4BN98_A0A2U4BN98_TURTR_9739 are exactly identical!
WARNING: Duplicate sequences found: 26

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00451/4_raxmlng_ancestral/P00451.raxml.reduced.phy

Alignment comprises 1 partitions and 2351 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 2351
Gaps: 64.11 %
Invariant sites: 0.04 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00451/4_raxmlng_ancestral/P00451.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00451/3_mltree/P00451.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 588 / 47040
[00:00:00] Data distribution: max. searches per worker: 1

Starting ML tree search with 1 distinct starting trees

[00:00:01] Tree #1, initial LogLikelihood: -501620.000023

[00:00:02 -501620.000023] Initial branch length optimization
[00:06:43 -495649.956706] Model parameter optimization (eps = 0.100000)

[00:15:12] Tree #1, final logLikelihood: -493766.582825


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.108920,0.379256) (0.100726,0.414855) (0.295874,0.621539) (0.494479,1.482382) 
   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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00451/4_raxmlng_ancestral/P00451.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00451/4_raxmlng_ancestral/P00451.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00451/4_raxmlng_ancestral/P00451.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00451/4_raxmlng_ancestral/P00451.raxml.log

Analysis started: 03-Jun-2021 03:26:32 / finished: 03-Jun-2021 03:42:15

Elapsed time: 943.097 seconds

Consumed energy: 83.115 Wh