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 12-Jul-2021 17:36:46 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/2_msa/Q9HCH5_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/3_mltree/Q9HCH5.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/4_raxmlng_ancestral/Q9HCH5 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626100606
  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/Q9HCH5/2_msa/Q9HCH5_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 934 sites

WARNING: Sequences tr_A0A1D5PAQ9_A0A1D5PAQ9_CHICK_9031 and tr_A0A226N661_A0A226N661_CALSU_9009 are exactly identical!
WARNING: Sequences tr_A0A1D5PAQ9_A0A1D5PAQ9_CHICK_9031 and tr_A0A226PAY6_A0A226PAY6_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2I3G2E9_A0A2I3G2E9_NOMLE_61853 and tr_A0A2I3NI95_A0A2I3NI95_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3G2E9_A0A2I3G2E9_NOMLE_61853 and tr_A0A2K5YD37_A0A2K5YD37_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3R0Z1_G3R0Z1_GORGO_9595 and tr_A0A2J8IWZ5_A0A2J8IWZ5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R0Z1_G3R0Z1_GORGO_9595 and sp_O00445_SYT5_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2RHT3_H2RHT3_PANTR_9598 and tr_A0A2R9CC23_A0A2R9CC23_PANPA_9597 are exactly identical!
WARNING: Sequences sp_Q96C24_SYTL4_HUMAN_9606 and tr_A0A2R8ZUW0_A0A2R8ZUW0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1LA08_G1LA08_AILME_9646 and tr_A0A384DMJ3_A0A384DMJ3_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G7Q2I2_G7Q2I2_MACFA_9541 and tr_A0A2K6CGW5_A0A2K6CGW5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7Q2I2_G7Q2I2_MACFA_9541 and tr_A0A2K5YC48_A0A2K5YC48_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7Q379_G7Q379_MACFA_9541 and tr_A0A096MNV2_A0A096MNV2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7Q379_G7Q379_MACFA_9541 and tr_A0A2K5MV24_A0A2K5MV24_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7Q379_G7Q379_MACFA_9541 and tr_A0A2K6D1C1_A0A2K6D1C1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7Q379_G7Q379_MACFA_9541 and tr_A0A2K5ZRI6_A0A2K5ZRI6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0A0MWK6_A0A0A0MWK6_PAPAN_9555 and tr_A0A2K6DYL4_A0A2K6DYL4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0A0MWK6_A0A0A0MWK6_PAPAN_9555 and tr_A0A2K5XLY6_A0A2K5XLY6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I0LZU1_A0A2I0LZU1_COLLI_8932 and tr_A0A1V4KG22_A0A1V4KG22_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1PA79_A0A0V1PA79_9BILA_92180 and tr_A0A0V0UA16_A0A0V0UA16_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1I7TWK1_A0A1I7TWK1_9PELO_1561998 and tr_A0A1I7TWK2_A0A1I7TWK2_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A226NHV1_A0A226NHV1_CALSU_9009 and tr_A0A226NXR2_A0A226NXR2_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2K5KPN9_A0A2K5KPN9_CERAT_9531 and tr_A0A2K6BX54_A0A2K6BX54_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2U3V3F1_A0A2U3V3F1_TURTR_9739 and tr_A0A2Y9PGD2_A0A2Y9PGD2_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U3W9U1_A0A2U3W9U1_ODORO_9708 and tr_A0A2U3Z1K3_A0A2U3Z1K3_LEPWE_9713 are exactly identical!
WARNING: Duplicate sequences found: 24

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/Q9HCH5/4_raxmlng_ancestral/Q9HCH5.raxml.reduced.phy

Alignment comprises 1 partitions and 934 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 934
Gaps: 50.69 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/4_raxmlng_ancestral/Q9HCH5.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/Q9HCH5/3_mltree/Q9HCH5.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 234 / 18720
[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: -317566.965551

[00:00:00 -317566.965551] Initial branch length optimization
[00:00:02 -286271.918960] Model parameter optimization (eps = 0.100000)

[00:01:30] Tree #1, final logLikelihood: -285235.495337


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.084279,0.375846) (0.056999,0.635238) (0.315778,0.539801) (0.542944,1.402832) 
   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/Q9HCH5/4_raxmlng_ancestral/Q9HCH5.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/4_raxmlng_ancestral/Q9HCH5.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/4_raxmlng_ancestral/Q9HCH5.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/4_raxmlng_ancestral/Q9HCH5.raxml.log

Analysis started: 12-Jul-2021 17:36:46 / finished: 12-Jul-2021 17:38:26

Elapsed time: 99.793 seconds

Consumed energy: 7.126 Wh