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 23-Jun-2021 00:36:18 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBP0/2_msa/Q9UBP0_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBP0/3_mltree/Q9UBP0.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBP0/4_raxmlng_ancestral/Q9UBP0 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1624397778
  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/030621_run/phylogeny-snakemake/results/Q9UBP0/2_msa/Q9UBP0_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 616 sites

WARNING: Sequences tr_M3Y1H7_M3Y1H7_MUSPF_9669 and tr_A0A2Y9K6L7_A0A2Y9K6L7_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A0D8JS25_A0A0D8JS25_COCIM_246410 and tr_E9CVC7_E9CVC7_COCPS_443226 are exactly identical!
WARNING: Sequences tr_A0A0D8JS25_A0A0D8JS25_COCIM_246410 and tr_A0A0J7AWI3_A0A0J7AWI3_COCIT_404692 are exactly identical!
WARNING: Sequences tr_G3S7R1_G3S7R1_GORGO_9595 and tr_H2P6J6_H2P6J6_PONAB_9601 are exactly identical!
WARNING: Sequences tr_H2QHQ4_H2QHQ4_PANTR_9598 and sp_Q9UBP0_SPAST_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_B0W0A7_B0W0A7_CULQU_7176 and tr_B0XF07_B0XF07_CULQU_7176 are exactly identical!
WARNING: Sequences tr_J4VQT6_J4VQT6_BEAB2_655819 and tr_A0A0A2V5A6_A0A0A2V5A6_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_A0A158NDM2_A0A158NDM2_ATTCE_12957 and tr_A0A151HZH7_A0A151HZH7_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A0E0HKC9_A0A0E0HKC9_ORYNI_4536 and tr_B8B1Z6_B8B1Z6_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0HKC9_A0A0E0HKC9_ORYNI_4536 and tr_A0A0E0PSZ8_A0A0E0PSZ8_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0HKC9_A0A0E0HKC9_ORYNI_4536 and tr_A0A0E0A4H3_A0A0E0A4H3_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0HKC9_A0A0E0HKC9_ORYNI_4536 and tr_Q658G8_Q658G8_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A2QLM2_A2QLM2_ASPNC_425011 and tr_A0A318ZYA1_A0A318ZYA1_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7MLA9_G7MLA9_MACMU_9544 and tr_G7P1S1_G7P1S1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7XM11_G7XM11_ASPKW_1033177 and tr_A0A146FAT5_A0A146FAT5_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F4W8A4_F4W8A4_ACREC_103372 and tr_A0A195EXI9_A0A195EXI9_9HYME_34720 are exactly identical!
WARNING: Sequences tr_G2YFV5_G2YFV5_BOTF4_999810 and tr_M7TXF0_M7TXF0_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_B3S0V7_B3S0V7_TRIAD_10228 and tr_A0A369SCZ6_A0A369SCZ6_9METZ_287889 are exactly identical!
WARNING: Sequences tr_A0A0D2XVZ9_A0A0D2XVZ9_FUSO4_426428 and tr_N4UA18_N4UA18_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_A0A0D2XVZ9_A0A0D2XVZ9_FUSO4_426428 and tr_X0D2J5_X0D2J5_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0D2XVZ9_A0A0D2XVZ9_FUSO4_426428 and tr_A0A2H3T818_A0A2H3T818_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_W2PS96_W2PS96_PHYPN_761204 and tr_W2G494_W2G494_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A067HDH4_A0A067HDH4_CITSI_2711 and tr_V4TXZ6_V4TXZ6_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067HDH4_A0A067HDH4_CITSI_2711 and tr_A0A2H5NQQ2_A0A2H5NQQ2_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0B4IC23_A0A0B4IC23_METMF_1276143 and tr_A0A0D9PCX4_A0A0D9PCX4_METAN_1291518 are exactly identical!
WARNING: Sequences tr_A0A2G3ACW9_A0A2G3ACW9_CAPAN_4072 and tr_A0A2G3DAB2_A0A2G3DAB2_CAPCH_80379 are exactly identical!
WARNING: Duplicate sequences found: 26

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBP0/4_raxmlng_ancestral/Q9UBP0.raxml.reduced.phy

Alignment comprises 1 partitions and 616 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 616
Gaps: 27.71 %
Invariant sites: 0.65 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBP0/4_raxmlng_ancestral/Q9UBP0.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/030621_run/phylogeny-snakemake/results/Q9UBP0/3_mltree/Q9UBP0.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 154 / 12320
[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: -274911.305168

[00:00:00 -274911.305168] Initial branch length optimization
[00:00:01 -260412.193901] Model parameter optimization (eps = 0.100000)

[00:00:55] Tree #1, final logLikelihood: -259501.012056


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.136595,0.103278) (0.172539,0.152739) (0.230330,0.673073) (0.460537,1.746898) 
   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/030621_run/phylogeny-snakemake/results/Q9UBP0/4_raxmlng_ancestral/Q9UBP0.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBP0/4_raxmlng_ancestral/Q9UBP0.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBP0/4_raxmlng_ancestral/Q9UBP0.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBP0/4_raxmlng_ancestral/Q9UBP0.raxml.log

Analysis started: 23-Jun-2021 00:36:18 / finished: 23-Jun-2021 00:37:18

Elapsed time: 60.951 seconds

Consumed energy: 5.104 Wh