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 15-Jul-2021 17:36:42 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14839/2_msa/Q14839_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14839/3_mltree/Q14839.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14839/4_raxmlng_ancestral/Q14839 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626359802
  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/300621_run/phylogeny-snakemake/results/Q14839/2_msa/Q14839_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1912 sites

WARNING: Sequences tr_M3Z1K2_M3Z1K2_MUSPF_9669 and tr_A0A2U3WHW2_A0A2U3WHW2_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Z1K2_M3Z1K2_MUSPF_9669 and tr_A0A2Y9K0Q8_A0A2Y9K0Q8_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3RRA9_G3RRA9_GORGO_9595 and tr_K7B9Z5_K7B9Z5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RRA9_G3RRA9_GORGO_9595 and tr_A0A2R9A4P1_A0A2R9A4P1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3RQ86_A0A2I3RQ86_PANTR_9598 and sp_O14647_CHD2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3RQ86_A0A2I3RQ86_PANTR_9598 and tr_G7MW02_G7MW02_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3RQ86_A0A2I3RQ86_PANTR_9598 and tr_G7P9H9_G7P9H9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A2I3RQ86_A0A2I3RQ86_PANTR_9598 and tr_A0A0D9RWR2_A0A0D9RWR2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3RQ86_A0A2I3RQ86_PANTR_9598 and tr_A0A2K5LN76_A0A2K5LN76_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A158N917_A0A158N917_ATTCE_12957 and tr_A0A195BVQ5_A0A195BVQ5_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A0E0HLU3_A0A0E0HLU3_ORYNI_4536 and tr_A0A0D3GDJ7_A0A0D3GDJ7_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_B8B5J6_B8B5J6_ORYSI_39946 and tr_A0A0E0QC99_A0A0E0QC99_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1QAU8_I1QAU8_ORYGL_4538 and tr_I1QWL9_I1QWL9_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0PUC5_A0A0E0PUC5_ORYRU_4529 and tr_A0A0E0A5X8_A0A0E0A5X8_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_G7P802_G7P802_MACFA_9541 and tr_A0A096MMS1_A0A096MMS1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7P802_G7P802_MACFA_9541 and tr_A0A0D9RS42_A0A0D9RS42_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7P802_G7P802_MACFA_9541 and tr_A0A2K5LU02_A0A2K5LU02_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7P802_G7P802_MACFA_9541 and tr_A0A2K6EAC4_A0A2K6EAC4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_V4UCK9_V4UCK9_9ROSI_85681 and tr_A0A2H5P9M3_A0A2H5P9M3_CITUN_55188 are exactly identical!
WARNING: Sequences tr_V4UCK9_V4UCK9_9ROSI_85681 and tr_A0A2H5P9N9_A0A2H5P9N9_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A2I0MDG8_A0A2I0MDG8_COLLI_8932 and tr_A0A1V4JED6_A0A1V4JED6_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A2H3C893_A0A2H3C893_9AGAR_1076256 and tr_A0A284QM25_A0A284QM25_9AGAR_47428 are exactly identical!
WARNING: Sequences tr_A0A2D0SQV4_A0A2D0SQV4_ICTPU_7998 and tr_A0A2D0SQV7_A0A2D0SQV7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U3ZLY1_A0A2U3ZLY1_ODORO_9708 and tr_A0A2U3X8Q8_A0A2U3X8Q8_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2U3ZLY1_A0A2U3ZLY1_ODORO_9708 and tr_A0A384CXB1_A0A384CXB1_URSMA_29073 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/300621_run/phylogeny-snakemake/results/Q14839/4_raxmlng_ancestral/Q14839.raxml.reduced.phy

Alignment comprises 1 partitions and 1912 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 1912
Gaps: 30.63 %
Invariant sites: 0.52 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14839/4_raxmlng_ancestral/Q14839.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/300621_run/phylogeny-snakemake/results/Q14839/3_mltree/Q14839.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 478 / 38240
[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: -509631.840786

[00:00:01 -509631.840786] Initial branch length optimization
[00:00:05 -489559.951272] Model parameter optimization (eps = 0.100000)

[00:01:43] Tree #1, final logLikelihood: -488738.761165


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.141990,0.174711) (0.122824,0.250142) (0.317906,0.683072) (0.417280,1.742996) 
   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/300621_run/phylogeny-snakemake/results/Q14839/4_raxmlng_ancestral/Q14839.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14839/4_raxmlng_ancestral/Q14839.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14839/4_raxmlng_ancestral/Q14839.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14839/4_raxmlng_ancestral/Q14839.raxml.log

Analysis started: 15-Jul-2021 17:36:42 / finished: 15-Jul-2021 17:38:45

Elapsed time: 122.687 seconds

Consumed energy: 9.815 Wh