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 19-Jun-2021 19:50:24 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P37058/2_msa/P37058_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P37058/3_mltree/P37058.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P37058/4_raxmlng_ancestral/P37058 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1624121424
  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_040621/phylogeny-snakemake/results/P37058/2_msa/P37058_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 310 sites

WARNING: Sequences tr_B4R687_B4R687_DROSI_7240 and tr_B4IL51_B4IL51_DROSE_7238 are exactly identical!
WARNING: Sequences sp_Q1DNC5_MKAR_COCIM_246410 and tr_A0A0J7B9B7_A0A0J7B9B7_COCIT_404692 are exactly identical!
WARNING: Sequences sp_B2WMJ3_MKAR_PYRTR_426418 and tr_A0A2W1DSB8_A0A2W1DSB8_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_Q29I25_Q29I25_DROPS_46245 and tr_B4H4J3_B4H4J3_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2Q3G0_H2Q3G0_PANTR_9598 and tr_A0A2R9C3H2_A0A2R9C3H2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_J4KLF8_J4KLF8_BEAB2_655819 and tr_A0A0A2VG12_A0A0A2VG12_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J4KLF8_J4KLF8_BEAB2_655819 and tr_A0A167EIA0_A0A167EIA0_9HYPO_1081107 are exactly identical!
WARNING: Sequences tr_A0A088A0P5_A0A088A0P5_APIME_7460 and tr_A0A2A3EP06_A0A2A3EP06_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158N9V4_A0A158N9V4_ATTCE_12957 and tr_A0A151I4D2_A0A151I4D2_9HYME_520822 are exactly identical!
WARNING: Sequences sp_Q2UET3_MKAR_ASPOR_510516 and tr_A0A1S9E0H0_A0A1S9E0H0_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A0E0GIN8_A0A0E0GIN8_ORYNI_4536 and tr_A2X6T4_A2X6T4_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0GIN8_A0A0E0GIN8_ORYNI_4536 and tr_I1P1V1_I1P1V1_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0GIN8_A0A0E0GIN8_ORYNI_4536 and tr_A0A0E0NHB4_A0A0E0NHB4_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GIN8_A0A0E0GIN8_ORYNI_4536 and tr_A0A0D9YUH6_A0A0D9YUH6_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A1D5RKB3_A0A1D5RKB3_MACMU_9544 and tr_G7PSR8_G7PSR8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G2XRT0_G2XRT0_BOTF4_999810 and tr_M7TWX9_M7TWX9_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_I3LJY8_I3LJY8_PIG_9823 and sp_Q5E9H7_DHB12_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_F2SQ71_F2SQ71_TRIRC_559305 and tr_A0A178EX87_A0A178EX87_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_B3RWI1_B3RWI1_TRIAD_10228 and tr_A0A369RTJ2_A0A369RTJ2_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G7PZV5_G7PZV5_MACFA_9541 and tr_A0A096N5G0_A0A096N5G0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PZV5_G7PZV5_MACFA_9541 and tr_A0A2K5LFZ1_A0A2K5LFZ1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F2PWQ3_F2PWQ3_TRIEC_559882 and tr_A0A059JE44_A0A059JE44_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_L0PD97_L0PD97_PNEJ8_1209962 and tr_A0A0W4ZSF5_A0A0W4ZSF5_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_N4UKN4_N4UKN4_FUSC1_1229664 and tr_X0CWX2_X0CWX2_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_N4UKN4_N4UKN4_FUSC1_1229664 and tr_A0A2H3TXQ7_A0A2H3TXQ7_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_N4UKN4_N4UKN4_FUSC1_1229664 and tr_A0A2H3GJ31_A0A2H3GJ31_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_N4UKN4_N4UKN4_FUSC1_1229664 and tr_A0A2K0WHG2_A0A2K0WHG2_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_M2T788_M2T788_COCSN_665912 and tr_M2TNL0_M2TNL0_COCH5_701091 are exactly identical!
WARNING: Sequences tr_W2PUW4_W2PUW4_PHYPN_761204 and tr_A0A0W8CFE7_A0A0W8CFE7_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A015IFK0_A0A015IFK0_9GLOM_1432141 and tr_U9V7K7_U9V7K7_RHIID_747089 are exactly identical!
WARNING: Sequences tr_V4VFW3_V4VFW3_9ROSI_85681 and tr_A0A2H5NV35_A0A2H5NV35_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0V0WKI1_A0A0V0WKI1_9BILA_92179 and tr_A0A0V1LP01_A0A0V1LP01_9BILA_6335 are exactly identical!
WARNING: Sequences tr_V6RIE5_V6RIE5_GIBZE_229533 and tr_A0A2T4GJG7_A0A2T4GJG7_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A1S3YCL6_A0A1S3YCL6_TOBAC_4097 and tr_A0A1U7VUH0_A0A1U7VUH0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3PFX5_A0A1S3PFX5_SALSA_8030 and tr_B5X752_B5X752_SALSA_8030 are exactly identical!
WARNING: Duplicate sequences found: 35

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P37058/4_raxmlng_ancestral/P37058.raxml.reduced.phy

Alignment comprises 1 partitions and 310 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 310
Gaps: 10.40 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P37058/4_raxmlng_ancestral/P37058.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_040621/phylogeny-snakemake/results/P37058/3_mltree/P37058.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 78 / 6240
[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: -184722.221027

[00:00:00 -184722.221027] Initial branch length optimization
[00:00:00 -184491.381612] Model parameter optimization (eps = 0.100000)

[00:00:23] Tree #1, final logLikelihood: -183588.733403


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.190258,0.403623) (0.235633,0.437034) (0.390396,1.187090) (0.183712,1.942124) 
   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_040621/phylogeny-snakemake/results/P37058/4_raxmlng_ancestral/P37058.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P37058/4_raxmlng_ancestral/P37058.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P37058/4_raxmlng_ancestral/P37058.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P37058/4_raxmlng_ancestral/P37058.raxml.log

Analysis started: 19-Jun-2021 19:50:24 / finished: 19-Jun-2021 19:50:50

Elapsed time: 26.630 seconds