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 14:10:41 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NI36/2_msa/Q8NI36_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NI36/3_mltree/Q8NI36.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NI36/4_raxmlng_ancestral/Q8NI36 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622805041
  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/Q8NI36/2_msa/Q8NI36_nogap_msa.fasta
[00:00:00] Loaded alignment with 979 taxa and 951 sites

WARNING: Sequences tr_B6GY70_B6GY70_PENRW_500485 and tr_K9FQV8_K9FQV8_PEND2_1170229 are exactly identical!
WARNING: Sequences tr_B6GY70_B6GY70_PENRW_500485 and tr_A0A0A2JWP1_A0A0A2JWP1_PENEN_27334 are exactly identical!
WARNING: Sequences tr_B6GY70_B6GY70_PENRW_500485 and tr_A0A0G4PVD2_A0A0G4PVD2_PENCA_1429867 are exactly identical!
WARNING: Sequences tr_B6GY70_B6GY70_PENRW_500485 and tr_A0A101MAS8_A0A101MAS8_9EURO_48697 are exactly identical!
WARNING: Sequences tr_B6GY70_B6GY70_PENRW_500485 and tr_A0A135LQC5_A0A135LQC5_PENPA_5078 are exactly identical!
WARNING: Sequences tr_B6GY70_B6GY70_PENRW_500485 and tr_A0A1V6N7L9_A0A1V6N7L9_9EURO_60169 are exactly identical!
WARNING: Sequences tr_B6QV72_B6QV72_TALMQ_441960 and tr_A0A093UW39_A0A093UW39_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WE72_B2WE72_PYRTR_426418 and tr_A0A2W1GBH3_A0A2W1GBH3_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_F9F299_F9F299_FUSOF_660025 and tr_X0D1Q3_X0D1Q3_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9F299_F9F299_FUSOF_660025 and tr_A0A2H3T303_A0A2H3T303_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9F299_F9F299_FUSOF_660025 and tr_A0A2H3H6F5_A0A2H3H6F5_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_F9FE28_F9FE28_FUSOF_660025 and tr_W7MDT9_W7MDT9_GIBM7_334819 are exactly identical!
WARNING: Sequences tr_F9FE28_F9FE28_FUSOF_660025 and tr_A0A0D2Y2N0_A0A0D2Y2N0_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FE28_F9FE28_FUSOF_660025 and tr_N4UFS4_N4UFS4_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FE28_F9FE28_FUSOF_660025 and tr_X0CMR2_X0CMR2_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_G7Y0Q0_G7Y0Q0_ASPKW_1033177 and tr_A0A146FXN2_A0A146FXN2_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F9XHP8_F9XHP8_ZYMTI_336722 and tr_A0A0F4GTS5_A0A0F4GTS5_9PEZI_1047168 are exactly identical!
WARNING: Sequences tr_F9XHP8_F9XHP8_ZYMTI_336722 and tr_A0A1X7S155_A0A1X7S155_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YZ28_G2YZ28_BOTF4_999810 and tr_M7UL62_M7UL62_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_S0E6F2_S0E6F2_GIBF5_1279085 and tr_A0A2H3T2Q8_A0A2H3T2Q8_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_S0E6F2_S0E6F2_GIBF5_1279085 and tr_A0A2K0VYE1_A0A2K0VYE1_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_A0A015MWM8_A0A015MWM8_9GLOM_1432141 and tr_U9UFS7_U9UFS7_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A067F179_A0A067F179_CITSI_2711 and tr_V4SAX6_V4SAX6_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067F179_A0A067F179_CITSI_2711 and tr_A0A2H5QGM9_A0A2H5QGM9_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A078G7D6_A0A078G7D6_BRANA_3708 and tr_A0A0D3B8G2_A0A0D3B8G2_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0F8V0E5_A0A0F8V0E5_9EURO_308745 and tr_A0A2T5LSD4_A0A2T5LSD4_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A1S3H174_A0A1S3H174_LINUN_7574 and tr_A0A1S3H3P4_A0A1S3H3P4_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A2V5IRH8_A0A2V5IRH8_9EURO_1450541 and tr_A0A2V5I467_A0A2V5I467_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 28

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/Q8NI36/4_raxmlng_ancestral/Q8NI36.raxml.reduced.phy

Alignment comprises 1 partitions and 951 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 951
Gaps: 27.97 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NI36/4_raxmlng_ancestral/Q8NI36.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/Q8NI36/3_mltree/Q8NI36.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 238 / 19040
[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: -466218.102793

[00:00:00 -466218.102793] Initial branch length optimization
[00:00:02 -462355.929105] Model parameter optimization (eps = 0.100000)

[00:01:11] Tree #1, final logLikelihood: -460858.663394


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.144419,0.506495) (0.235368,0.531939) (0.378874,0.843927) (0.241339,1.996814) 
   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/Q8NI36/4_raxmlng_ancestral/Q8NI36.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NI36/4_raxmlng_ancestral/Q8NI36.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NI36/4_raxmlng_ancestral/Q8NI36.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NI36/4_raxmlng_ancestral/Q8NI36.raxml.log

Analysis started: 04-Jun-2021 14:10:41 / finished: 04-Jun-2021 14:12:01

Elapsed time: 79.288 seconds