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 01:37:31 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P01130/2_msa/P01130_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P01130/3_mltree/P01130.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P01130/4_raxmlng_ancestral/P01130 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622673451
  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/P01130/2_msa/P01130_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 860 sites

WARNING: Sequences tr_B4QVD9_B4QVD9_DROSI_7240 and tr_B4ICD1_B4ICD1_DROSE_7238 are exactly identical!
WARNING: Sequences tr_M3XRN5_M3XRN5_MUSPF_9669 and tr_G1LDK5_G1LDK5_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3XRN5_M3XRN5_MUSPF_9669 and tr_A0A2Y9LB05_A0A2Y9LB05_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3R3Z1_G3R3Z1_GORGO_9595 and tr_A0A2I3S3K1_A0A2I3S3K1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R3Z1_G3R3Z1_GORGO_9595 and tr_A0A2R9A7D0_A0A2R9A7D0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RKG1_G3RKG1_GORGO_9595 and sp_P98164_LRP2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_B5DYP7_B5DYP7_DROPS_46245 and tr_B4GFZ1_B4GFZ1_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2QIS5_H2QIS5_PANTR_9598 and tr_A0A2R8ZC47_A0A2R8ZC47_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6WNN2_F6WNN2_MACMU_9544 and tr_A0A2K6DIN8_A0A2K6DIN8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6WNN2_F6WNN2_MACMU_9544 and tr_A0A2K5YLT6_A0A2K5YLT6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6YL51_F6YL51_MACMU_9544 and tr_A0A2K6E6H2_A0A2K6E6H2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H9EMK7_H9EMK7_MACMU_9544 and tr_A0A2K5P451_A0A2K5P451_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H9EMK7_H9EMK7_MACMU_9544 and tr_A0A2K6C2A3_A0A2K6C2A3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H9EMK7_H9EMK7_MACMU_9544 and tr_A0A2K5ZXC9_A0A2K5ZXC9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_M3X7K5_M3X7K5_FELCA_9685 and tr_A0A2Y9SMR1_A0A2Y9SMR1_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_M3X7K5_M3X7K5_FELCA_9685 and tr_A0A383ZX51_A0A383ZX51_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A0V1CJN0_A0A0V1CJN0_TRIBR_45882 and tr_A0A0V0W5R7_A0A0V0W5R7_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1CJN0_A0A0V1CJN0_TRIBR_45882 and tr_A0A0V0VAW0_A0A0V0VAW0_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CJN0_A0A0V1CJN0_TRIBR_45882 and tr_A0A0V1L3G8_A0A0V1L3G8_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1CJN0_A0A0V1CJN0_TRIBR_45882 and tr_A0A0V0TGX4_A0A0V0TGX4_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1D5C2_A0A0V1D5C2_TRIBR_45882 and tr_A0A0V1LAG3_A0A0V1LAG3_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1D5C2_A0A0V1D5C2_TRIBR_45882 and tr_A0A0V1A039_A0A0V1A039_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0WGS4_A0A0V0WGS4_9BILA_92179 and tr_A0A0V1LFU4_A0A0V1LFU4_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1P7W8_A0A0V1P7W8_9BILA_92180 and tr_A0A0V0TQN3_A0A0V0TQN3_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A2D0S0V8_A0A2D0S0V8_ICTPU_7998 and tr_A0A2D0S1J5_A0A2D0S1J5_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 25

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/P01130/4_raxmlng_ancestral/P01130.raxml.reduced.phy

Alignment comprises 1 partitions and 860 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 860
Gaps: 11.87 %
Invariant sites: 0.12 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P01130/4_raxmlng_ancestral/P01130.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/P01130/3_mltree/P01130.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 215 / 17200
[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: -330130.631670

[00:00:00 -330130.631670] Initial branch length optimization
[00:00:01 -327717.477735] Model parameter optimization (eps = 0.100000)

[00:00:43] Tree #1, final logLikelihood: -327240.530087


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.162334,0.226399) (0.190981,0.415047) (0.410751,1.012028) (0.235934,1.984833) 
   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/P01130/4_raxmlng_ancestral/P01130.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P01130/4_raxmlng_ancestral/P01130.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P01130/4_raxmlng_ancestral/P01130.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P01130/4_raxmlng_ancestral/P01130.raxml.log

Analysis started: 03-Jun-2021 01:37:31 / finished: 03-Jun-2021 01:38:22

Elapsed time: 51.235 seconds

Consumed energy: 4.021 Wh