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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 02-Jun-2021 18:24:11 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15147/2_msa/Q15147_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15147/3_mltree/Q15147.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15147/4_raxmlng_ancestral/Q15147 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622647451
  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/Q15147/2_msa/Q15147_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1175 sites

WARNING: Sequences tr_A0A2I2Z963_A0A2I2Z963_GORGO_9595 and tr_K7BA21_K7BA21_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2Z963_A0A2I2Z963_GORGO_9595 and sp_Q9NQ66_PLCB1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2Z963_A0A2I2Z963_GORGO_9595 and tr_A0A2R8ZNS9_A0A2R8ZNS9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2PBD1_H2PBD1_PONAB_9601 and tr_A0A2I3RKF6_A0A2I3RKF6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2PBD1_H2PBD1_PONAB_9601 and sp_Q9UPR0_PLCL2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PBD1_H2PBD1_PONAB_9601 and tr_A0A0D9RC42_A0A0D9RC42_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2PBD1_H2PBD1_PONAB_9601 and tr_A0A2K5L983_A0A2K5L983_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3RV12_A0A2I3RV12_PANTR_9598 and tr_A0A2R9C5Q7_A0A2R9C5Q7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3T8F7_A0A2I3T8F7_PANTR_9598 and tr_A0A2R9CAD8_A0A2R9CAD8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2J8QDF6_A0A2J8QDF6_PANTR_9598 and tr_A0A2R9BYE2_A0A2R9BYE2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QJY5_H2QJY5_PANTR_9598 and tr_A0A2R8ZPT1_A0A2R8ZPT1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6ZKL2_F6ZKL2_MACMU_9544 and tr_A0A2K6E7S8_A0A2K6E7S8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7GVF8_F7GVF8_MACMU_9544 and tr_A0A2K6CKD4_A0A2K6CKD4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H9FVW1_H9FVW1_MACMU_9544 and tr_A0A0D9RMD0_A0A0D9RMD0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H9FVW1_H9FVW1_MACMU_9544 and tr_A0A2K6BBP9_A0A2K6BBP9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H0YY72_H0YY72_TAEGU_59729 and tr_A0A218VEW1_A0A218VEW1_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A1B8Y9Z8_A0A1B8Y9Z8_XENTR_8364 and tr_F6V4E2_F6V4E2_XENTR_8364 are exactly identical!
WARNING: Sequences tr_U3K9D5_U3K9D5_FICAL_59894 and tr_A0A091F5K6_A0A091F5K6_CORBR_85066 are exactly identical!
WARNING: Sequences tr_A0A2D0Q0H0_A0A2D0Q0H0_ICTPU_7998 and tr_A0A2D0Q263_A0A2D0Q263_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0Q0H0_A0A2D0Q0H0_ICTPU_7998 and tr_A0A2D0Q267_A0A2D0Q267_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0Q0H0_A0A2D0Q0H0_ICTPU_7998 and tr_A0A2D0Q338_A0A2D0Q338_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5M3I3_A0A2K5M3I3_CERAT_9531 and tr_A0A2K6AJD5_A0A2K6AJD5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5XAK8_A0A2K5XAK8_MANLE_9568 and tr_A0A2R8ZE07_A0A2R8ZE07_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2U4BV49_A0A2U4BV49_TURTR_9739 and tr_A0A2Y9LS93_A0A2Y9LS93_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4BV49_A0A2U4BV49_TURTR_9739 and tr_A0A2Y9SSJ8_A0A2Y9SSJ8_PHYCD_9755 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/Q15147/4_raxmlng_ancestral/Q15147.raxml.reduced.phy

Alignment comprises 1 partitions and 1175 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 1175
Gaps: 25.02 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15147/4_raxmlng_ancestral/Q15147.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/Q15147/3_mltree/Q15147.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 294 / 23520
[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: -363703.082429

[00:00:00 -363703.082429] Initial branch length optimization
[00:00:02 -356865.962223] Model parameter optimization (eps = 0.100000)

[00:00:59] Tree #1, final logLikelihood: -356124.271748


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.129503,0.237933) (0.156013,0.320628) (0.361434,0.774547) (0.353050,1.810558) 
   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/Q15147/4_raxmlng_ancestral/Q15147.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15147/4_raxmlng_ancestral/Q15147.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15147/4_raxmlng_ancestral/Q15147.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15147/4_raxmlng_ancestral/Q15147.raxml.log

Analysis started: 02-Jun-2021 18:24:11 / finished: 02-Jun-2021 18:25:22

Elapsed time: 70.599 seconds

Consumed energy: 3.667 Wh