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 02-Jun-2021 18:52:18 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05787/2_msa/P05787_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05787/3_mltree/P05787.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05787/4_raxmlng_ancestral/P05787 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622649138
  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/P05787/2_msa/P05787_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 483 sites

WARNING: Sequences sp_Q9DCV7_K2C7_MOUSE_10090 and sp_Q6IG12_K2C7_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3Y7A1_M3Y7A1_MUSPF_9669 and tr_A0A2U3VZ44_A0A2U3VZ44_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Y7A1_M3Y7A1_MUSPF_9669 and tr_A0A2Y9KMA6_A0A2Y9KMA6_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3QJY7_G3QJY7_GORGO_9595 and tr_H2Q5Z3_H2Q5Z3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QLP7_G3QLP7_GORGO_9595 and sp_P04264_K2C1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1SY72_G1SY72_RABIT_9986 and sp_Q29426_K2C3_RABIT_9986 are exactly identical!
WARNING: Sequences tr_F1PTY1_F1PTY1_CANLF_9615 and sp_Q6EIY9_K2C1_CANLF_9615 are exactly identical!
WARNING: Sequences tr_A0A2I3TV17_A0A2I3TV17_PANTR_9598 and sp_P12035_K2C3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2J8KDC3_A0A2J8KDC3_PANTR_9598 and tr_A0A2R9A6T6_A0A2R9A6T6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2J8KDF1_A0A2J8KDF1_PANTR_9598 and tr_A0A2R9CPA3_A0A2R9CPA3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5QLK5_A0A1D5QLK5_MACMU_9544 and tr_A0A096MW83_A0A096MW83_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QLK5_A0A1D5QLK5_MACMU_9544 and tr_A0A2K5P6H0_A0A2K5P6H0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QLK5_A0A1D5QLK5_MACMU_9544 and tr_A0A2K6B230_A0A2K6B230_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QLK5_A0A1D5QLK5_MACMU_9544 and tr_A0A2K5XMZ6_A0A2K5XMZ6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6VKQ3_F6VKQ3_MACMU_9544 and tr_A0A2K6DMD1_A0A2K6DMD1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7AEN7_F7AEN7_MACMU_9544 and tr_A0A2K6BPE2_A0A2K6BPE2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7E5G8_F7E5G8_MACMU_9544 and tr_A0A2K6B509_A0A2K6B509_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HGY2_F7HGY2_MACMU_9544 and tr_A0A2K6CR37_A0A2K6CR37_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HME7_F7HME7_MACMU_9544 and tr_A0A2K5N2V1_A0A2K5N2V1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A5D7M6_A5D7M6_BOVIN_9913 and sp_Q5XQN5_K2C5_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A096MPX0_A0A096MPX0_PAPAN_9555 and tr_A0A2K5LH62_A0A2K5LH62_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096MVH8_A0A096MVH8_PAPAN_9555 and tr_A0A2K5ZK75_A0A2K5ZK75_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096N7Y8_A0A096N7Y8_PAPAN_9555 and tr_A0A2K5NJ30_A0A2K5NJ30_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096N7Y8_A0A096N7Y8_PAPAN_9555 and tr_A0A2K6E7G3_A0A2K6E7G3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096N7Y8_A0A096N7Y8_PAPAN_9555 and tr_A0A2K5XF23_A0A2K5XF23_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096N9P6_A0A096N9P6_PAPAN_9555 and tr_A0A2K6AE66_A0A2K6AE66_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096NAU0_A0A096NAU0_PAPAN_9555 and tr_A0A2K5MDQ1_A0A2K5MDQ1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NAU0_A0A096NAU0_PAPAN_9555 and tr_A0A2K6CZV9_A0A2K6CZV9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2K5MWZ1_A0A2K5MWZ1_CERAT_9531 and tr_A0A2K6AJW7_A0A2K6AJW7_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 29

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/P05787/4_raxmlng_ancestral/P05787.raxml.reduced.phy

Alignment comprises 1 partitions and 483 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 483
Gaps: 11.39 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05787/4_raxmlng_ancestral/P05787.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/P05787/3_mltree/P05787.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 121 / 9680
[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: -142405.187467

[00:00:00 -142405.187467] Initial branch length optimization
[00:00:01 -142104.295023] Model parameter optimization (eps = 0.100000)

[00:00:40] Tree #1, final logLikelihood: -141363.860647


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.287589,0.463778) (0.189178,0.736368) (0.388709,1.225930) (0.134525,1.864259) 
   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/P05787/4_raxmlng_ancestral/P05787.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05787/4_raxmlng_ancestral/P05787.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05787/4_raxmlng_ancestral/P05787.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05787/4_raxmlng_ancestral/P05787.raxml.log

Analysis started: 02-Jun-2021 18:52:18 / finished: 02-Jun-2021 18:53:03

Elapsed time: 45.066 seconds

Consumed energy: 3.591 Wh