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 14-Jul-2021 13:38:32 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96C36/2_msa/Q96C36_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96C36/3_mltree/Q96C36.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96C36/4_raxmlng_ancestral/Q96C36 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626259112
  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_300621/phylogeny-snakemake/results/Q96C36/2_msa/Q96C36_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 320 sites

WARNING: Sequences tr_A0A0E1RXP3_A0A0E1RXP3_COCIM_246410 and tr_A0A0J6YEZ7_A0A0J6YEZ7_COCIT_404692 are exactly identical!
WARNING: Sequences sp_Q5R9X6_P5CR1_PONAB_9601 and sp_P32322_P5CR1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_Q29BT4_Q29BT4_DROPS_46245 and tr_B4GPN9_B4GPN9_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B8N5R2_B8N5R2_ASPFN_332952 and tr_Q2UDM2_Q2UDM2_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_H2QWU6_H2QWU6_PANTR_9598 and sp_Q53H96_P5CR3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R2L7_H2R2L7_PANTR_9598 and tr_A0A2R9BXD4_A0A2R9BXD4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7AGU5_K7AGU5_PANTR_9598 and tr_A0A2R9ABC1_A0A2R9ABC1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0B4J2M9_A0A0B4J2M9_APIME_7460 and tr_A0A2A3E4E4_A0A2A3E4E4_APICC_94128 are exactly identical!
WARNING: Sequences tr_A2QIA2_A2QIA2_ASPNC_425011 and tr_A0A319AHE7_A0A319AHE7_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F7FLW2_F7FLW2_MACMU_9544 and tr_A0A096NFP1_A0A096NFP1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7FLW2_F7FLW2_MACMU_9544 and tr_A0A2K6ANH6_A0A2K6ANH6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7FLW2_F7FLW2_MACMU_9544 and tr_A0A2K5XG63_A0A2K5XG63_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7X7H8_G7X7H8_ASPKW_1033177 and tr_A0A146FIM3_A0A146FIM3_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_I1NV79_I1NV79_ORYGL_4538 and tr_A0A0E0N7M0_A0A0E0N7M0_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_E6R8L9_E6R8L9_CRYGW_367775 and tr_A0A095C4R5_A0A095C4R5_CRYGR_294750 are exactly identical!
WARNING: Sequences tr_A8XNV3_A8XNV3_CAEBR_6238 and tr_A0A2G5SL38_A0A2G5SL38_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_V2YYU9_V2YYU9_MONRO_1381753 and tr_A0A0W0F8W1_A0A0W0F8W1_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2QK11_W2QK11_PHYPN_761204 and tr_A0A0W8CXX0_A0A0W8CXX0_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QK11_W2QK11_PHYPN_761204 and tr_W2LQ04_W2LQ04_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015L3Y5_A0A015L3Y5_9GLOM_1432141 and tr_A0A2I1G7C0_A0A2I1G7C0_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_X0CF54_X0CF54_FUSOX_1089458 and tr_A0A2H3TMM5_A0A2H3TMM5_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_V4S6N7_V4S6N7_9ROSI_85681 and tr_A0A2H5PQY4_A0A2H5PQY4_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0A1N921_A0A0A1N921_9FUNG_58291 and tr_A0A367JCB8_A0A367JCB8_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0A1NJJ5_A0A0A1NJJ5_9FUNG_58291 and tr_A0A367JF52_A0A367JF52_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0A1NKC8_A0A0A1NKC8_9FUNG_58291 and tr_A0A367J1Y6_A0A367J1Y6_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0A1NYW7_A0A0A1NYW7_9FUNG_58291 and tr_A0A367JG70_A0A367JG70_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0V1DGR9_A0A0V1DGR9_TRIBR_45882 and tr_A0A0V1P8R2_A0A0V1P8R2_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A100IAC0_A0A100IAC0_ASPNG_5061 and tr_A0A1L9MWU3_A0A1L9MWU3_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A165AM38_A0A165AM38_9HOMO_1314777 and tr_A0A166GW78_A0A166GW78_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1D1VV69_A0A1D1VV69_RAMVA_947166 and tr_A0A1D1VV70_A0A1D1VV70_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A1D1VV69_A0A1D1VV69_RAMVA_947166 and tr_A0A1D1VWS2_A0A1D1VWS2_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A2K5L7A1_A0A2K5L7A1_CERAT_9531 and tr_A0A2K6AD82_A0A2K6AD82_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5P6J4_A0A2K5P6J4_CERAT_9531 and tr_A0A2K5ZNJ2_A0A2K5ZNJ2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2V5IGC1_A0A2V5IGC1_9EURO_1450541 and tr_A0A2V5I934_A0A2V5I934_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 34

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96C36/4_raxmlng_ancestral/Q96C36.raxml.reduced.phy

Alignment comprises 1 partitions and 320 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 320
Gaps: 17.30 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96C36/4_raxmlng_ancestral/Q96C36.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_300621/phylogeny-snakemake/results/Q96C36/3_mltree/Q96C36.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 80 / 6400
[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: -150325.943566

[00:00:00 -150325.943566] Initial branch length optimization
[00:00:01 -149309.933839] Model parameter optimization (eps = 0.100000)

[00:00:23] Tree #1, final logLikelihood: -148716.173354


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.168897,0.311842) (0.250535,0.370815) (0.305223,0.831889) (0.275345,2.180960) 
   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_300621/phylogeny-snakemake/results/Q96C36/4_raxmlng_ancestral/Q96C36.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96C36/4_raxmlng_ancestral/Q96C36.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96C36/4_raxmlng_ancestral/Q96C36.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96C36/4_raxmlng_ancestral/Q96C36.raxml.log

Analysis started: 14-Jul-2021 13:38:32 / finished: 14-Jul-2021 13:38:59

Elapsed time: 26.172 seconds