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 17-Jul-2021 08:22:47 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/2_msa/Q9UBH6_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/3_mltree/Q9UBH6.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/4_raxmlng_ancestral/Q9UBH6 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626499367
  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/Q9UBH6/2_msa/Q9UBH6_nogap_msa.fasta
[00:00:00] Loaded alignment with 987 taxa and 696 sites

WARNING: Sequences tr_B4QIU5_B4QIU5_DROSI_7240 and tr_B4HUL2_B4HUL2_DROSE_7238 are exactly identical!
WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_H2Q0Q1_H2Q0Q1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and sp_Q9UBH6_XPR1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_A0A2R8ZLI4_A0A2R8ZLI4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q29E65_Q29E65_DROPS_46245 and tr_B4HAV0_B4HAV0_DROPE_7234 are exactly identical!
WARNING: Sequences tr_F9FC72_F9FC72_FUSOF_660025 and tr_X0D0Z8_X0D0Z8_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_G7MF56_G7MF56_MACMU_9544 and tr_A0A2K5N6D4_A0A2K5N6D4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7MF56_G7MF56_MACMU_9544 and tr_A0A2K6C4X2_A0A2K6C4X2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7MF56_G7MF56_MACMU_9544 and tr_A0A2K5ZXB9_A0A2K5ZXB9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7XGZ3_G7XGZ3_ASPKW_1033177 and tr_A0A146F1A4_A0A146F1A4_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_B8AEH8_B8AEH8_ORYSI_39946 and tr_I1P5E0_I1P5E0_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_B8AEH8_B8AEH8_ORYSI_39946 and sp_Q6K991_PHO12_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_M4E7M7_M4E7M7_BRARP_51351 and tr_A0A078I6Y4_A0A078I6Y4_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4F566_M4F566_BRARP_51351 and tr_A0A078G3L2_A0A078G3L2_BRANA_3708 are exactly identical!
WARNING: Sequences tr_N4UIF6_N4UIF6_FUSC1_1229664 and tr_A0A2H3T8Y3_A0A2H3T8Y3_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A0A015JCH2_A0A015JCH2_9GLOM_1432141 and tr_A0A2H5SD87_A0A2H5SD87_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A067EEZ7_A0A067EEZ7_CITSI_2711 and tr_A0A2H5NV30_A0A2H5NV30_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A067FS23_A0A067FS23_CITSI_2711 and tr_V4ST36_V4ST36_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A078J482_A0A078J482_BRANA_3708 and tr_A0A0D3E7N7_A0A0D3E7N7_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A094GG97_A0A094GG97_9PEZI_1420912 and tr_A0A1B8GLD4_A0A1B8GLD4_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0V1DGY5_A0A0V1DGY5_TRIBR_45882 and tr_A0A0V0XC63_A0A0V0XC63_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1DGY5_A0A0V1DGY5_TRIBR_45882 and tr_A0A0V0VN33_A0A0V0VN33_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1DGY5_A0A0V1DGY5_TRIBR_45882 and tr_A0A0V0UC85_A0A0V0UC85_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S4B309_A0A1S4B309_TOBAC_4097 and tr_A0A1U7X944_A0A1U7X944_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2U1QG66_A0A2U1QG66_ARTAN_35608 and tr_A0A2U1QNQ7_A0A2U1QNQ7_ARTAN_35608 are exactly identical!
WARNING: Sequences tr_A0A2V5IAU5_A0A2V5IAU5_9EURO_1450541 and tr_A0A2V5I377_A0A2V5I377_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 26

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/Q9UBH6/4_raxmlng_ancestral/Q9UBH6.raxml.reduced.phy

Alignment comprises 1 partitions and 696 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 696
Gaps: 26.97 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/4_raxmlng_ancestral/Q9UBH6.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/Q9UBH6/3_mltree/Q9UBH6.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 174 / 13920
[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: -332611.561213

[00:00:00 -332611.561213] Initial branch length optimization
[00:00:02 -316959.015142] Model parameter optimization (eps = 0.100000)

[00:01:56] Tree #1, final logLikelihood: -315321.266132


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.143003,0.505945) (0.219415,0.895730) (0.337813,0.679267) (0.299768,1.673446) 
   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/Q9UBH6/4_raxmlng_ancestral/Q9UBH6.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/4_raxmlng_ancestral/Q9UBH6.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/4_raxmlng_ancestral/Q9UBH6.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/4_raxmlng_ancestral/Q9UBH6.raxml.log

Analysis started: 17-Jul-2021 08:22:47 / finished: 17-Jul-2021 08:24:49

Elapsed time: 122.389 seconds