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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 04-Jun-2021 13:56:43 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q03519/2_msa/Q03519_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q03519/3_mltree/Q03519.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q03519/4_raxmlng_ancestral/Q03519 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622804203
  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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q03519/2_msa/Q03519_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 686 sites

WARNING: Sequences tr_J3KLC8_J3KLC8_COCIM_246410 and tr_A0A0J6YQI9_A0A0J6YQI9_COCIT_404692 are exactly identical!
WARNING: Sequences tr_G3S798_G3S798_GORGO_9595 and sp_Q9NRK6_ABCBA_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q751_H2Q751_PANTR_9598 and sp_Q9NP78_ABCB9_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q751_H2Q751_PANTR_9598 and tr_A0A2R9CJZ3_A0A2R9CJZ3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9F932_F9F932_FUSOF_660025 and tr_N4TUX9_N4TUX9_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9F932_F9F932_FUSOF_660025 and tr_X0CAT2_X0CAT2_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9F932_F9F932_FUSOF_660025 and tr_A0A2H3SXP6_A0A2H3SXP6_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9F932_F9F932_FUSOF_660025 and tr_A0A2H3HI99_A0A2H3HI99_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A0E0GTY4_A0A0E0GTY4_ORYNI_4536 and tr_A0A0E0D6Z1_A0A0E0D6Z1_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0GTY4_A0A0E0GTY4_ORYNI_4536 and tr_A0A0D3FP85_A0A0D3FP85_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A2QJH1_A2QJH1_ASPNC_425011 and tr_G3Y9P6_G3Y9P6_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_G7XXM7_G7XXM7_ASPKW_1033177 and tr_A0A146FJZ8_A0A146FJZ8_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_B8AK86_B8AK86_ORYSI_39946 and sp_Q9FNU2_AB25B_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G2YK02_G2YK02_BOTF4_999810 and tr_M7UN73_M7UN73_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SVA7_F2SVA7_TRIRC_559305 and tr_D4AJ67_D4AJ67_ARTBC_663331 are exactly identical!
WARNING: Sequences tr_F2SVA7_F2SVA7_TRIRC_559305 and tr_A0A178F6E0_A0A178F6E0_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_B3S545_B3S545_TRIAD_10228 and tr_A0A369SHY0_A0A369SHY0_9METZ_287889 are exactly identical!
WARNING: Sequences tr_W7M6F2_W7M6F2_GIBM7_334819 and tr_A0A2K0WRA2_A0A2K0WRA2_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_G7P213_G7P213_MACFA_9541 and tr_A0A2K6DYQ7_A0A2K6DYQ7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G8F535_G8F535_MACFA_9541 and tr_A0A096N2X5_A0A096N2X5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G8F535_G8F535_MACFA_9541 and tr_A0A0D9S514_A0A0D9S514_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G8F535_G8F535_MACFA_9541 and tr_A0A2K6CNU3_A0A2K6CNU3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_S0EGW9_S0EGW9_GIBF5_1279085 and tr_A0A365MZ72_A0A365MZ72_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_W2Q091_W2Q091_PHYPN_761204 and tr_W2KW73_W2KW73_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A078HJ41_A0A078HJ41_BRANA_3708 and tr_A0A0D3BZR8_A0A0D3BZR8_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A100IBI3_A0A100IBI3_ASPNG_5061 and tr_A0A1L9MVB1_A0A1L9MVB1_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_I1RE13_I1RE13_GIBZE_229533 and tr_A0A2T4H774_A0A2T4H774_FUSCU_5516 are exactly identical!
WARNING: Duplicate sequences found: 27

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q03519/4_raxmlng_ancestral/Q03519.raxml.reduced.phy

Alignment comprises 1 partitions and 686 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 686
Gaps: 13.40 %
Invariant sites: 0.15 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q03519/4_raxmlng_ancestral/Q03519.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q03519/3_mltree/Q03519.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 172 / 13760
[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: -300103.574788

[00:00:00 -300103.574788] Initial branch length optimization
[00:00:01 -299492.765663] Model parameter optimization (eps = 0.100000)

[00:00:40] Tree #1, final logLikelihood: -298541.988733


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.195568,0.357112) (0.261169,0.427270) (0.357485,1.115759) (0.185778,2.259170) 
   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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q03519/4_raxmlng_ancestral/Q03519.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q03519/4_raxmlng_ancestral/Q03519.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q03519/4_raxmlng_ancestral/Q03519.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q03519/4_raxmlng_ancestral/Q03519.raxml.log

Analysis started: 04-Jun-2021 13:56:43 / finished: 04-Jun-2021 13:57:30

Elapsed time: 46.461 seconds