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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 03-Jun-2021 02:56:37 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q03426/2_msa/Q03426_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q03426/3_mltree/Q03426.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q03426/4_raxmlng_ancestral/Q03426 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622678197
  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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q03426/2_msa/Q03426_nogap_msa.fasta
[00:00:00] Loaded alignment with 951 taxa and 396 sites

WARNING: Sequences tr_Q1K7Q1_Q1K7Q1_NEUCR_367110 and tr_G4UHK8_G4UHK8_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_B5DZ21_B5DZ21_DROPS_46245 and tr_B4GD08_B4GD08_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B8N9Q8_B8N9Q8_ASPFN_332952 and tr_Q2UGL9_Q2UGL9_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8N9Q8_B8N9Q8_ASPFN_332952 and tr_A0A1S9DZ45_A0A1S9DZ45_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UBS2_A0A179UBS2_BLAGS_559298 and tr_C5GHJ0_C5GHJ0_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2Q6U7_H2Q6U7_PANTR_9598 and tr_A0A2R9CMF3_A0A2R9CMF3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FDR8_F9FDR8_FUSOF_660025 and tr_A0A0D2XUE0_A0A0D2XUE0_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FDR8_F9FDR8_FUSOF_660025 and tr_N4UFJ8_N4UFJ8_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FDR8_F9FDR8_FUSOF_660025 and tr_X0D0X9_X0D0X9_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FDR8_F9FDR8_FUSOF_660025 and tr_A0A2H3T494_A0A2H3T494_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_J4KM26_J4KM26_BEAB2_655819 and tr_A0A0A2VTX6_A0A0A2VTX6_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J4KM26_J4KM26_BEAB2_655819 and tr_A0A2N6NPE1_A0A2N6NPE1_BEABA_176275 are exactly identical!
WARNING: Sequences tr_F7HGV8_F7HGV8_MACMU_9544 and tr_G7PI68_G7PI68_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7HGV8_F7HGV8_MACMU_9544 and tr_A0A2K6DU94_A0A2K6DU94_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7X6T8_G7X6T8_ASPKW_1033177 and tr_A0A124BVY2_A0A124BVY2_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7X6T8_G7X6T8_ASPKW_1033177 and tr_A0A146FHH9_A0A146FHH9_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F4P4G0_F4P4G0_BATDJ_684364 and tr_A0A177WGA7_A0A177WGA7_BATDE_403673 are exactly identical!
WARNING: Sequences tr_I1QTG2_I1QTG2_ORYGL_4538 and tr_A0A0E0QXL7_A0A0E0QXL7_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1QTG2_I1QTG2_ORYGL_4538 and tr_Q339V1_Q339V1_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_D4AY19_D4AY19_ARTBC_663331 and tr_A0A059J8D1_A0A059J8D1_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_G0RGP4_G0RGP4_HYPJQ_431241 and tr_A0A2T4CAP8_A0A2T4CAP8_TRILO_983965 are exactly identical!
WARNING: Sequences tr_V2XF17_V2XF17_MONRO_1381753 and tr_A0A0W0FSS4_A0A0W0FSS4_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A015L7P9_A0A015L7P9_9GLOM_1432141 and tr_A0A2H5TIE6_A0A2H5TIE6_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0A1N2Y4_A0A0A1N2Y4_9FUNG_58291 and tr_A0A367JTM1_A0A367JTM1_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0V0SGP3_A0A0V0SGP3_9BILA_6336 and tr_A0A0V1AEB4_A0A0V1AEB4_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A1S3XMI2_A0A1S3XMI2_TOBAC_4097 and tr_A0A1U7YQX8_A0A1U7YQX8_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1I7UMY5_A0A1I7UMY5_9PELO_1561998 and tr_A0A1I7UMY6_A0A1I7UMY6_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A2H3BXC4_A0A2H3BXC4_9AGAR_1076256 and tr_A0A284QU97_A0A284QU97_9AGAR_47428 are exactly identical!
WARNING: Sequences tr_A0A2N5T8C2_A0A2N5T8C2_9BASI_200324 and tr_A0A2N5VYX8_A0A2N5VYX8_9BASI_200324 are exactly identical!
WARNING: Duplicate sequences found: 29

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q03426/4_raxmlng_ancestral/Q03426.raxml.reduced.phy

Alignment comprises 1 partitions and 396 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 396
Gaps: 13.34 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q03426/4_raxmlng_ancestral/Q03426.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q03426/3_mltree/Q03426.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 99 / 7920
[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: -208090.711157

[00:00:00 -208090.711157] Initial branch length optimization
[00:00:01 -207262.943602] Model parameter optimization (eps = 0.100000)

[00:00:16] Tree #1, final logLikelihood: -207236.436831


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.121829,0.107239) (0.258188,0.373310) (0.246807,0.783029) (0.373177,1.868537) 
   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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q03426/4_raxmlng_ancestral/Q03426.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q03426/4_raxmlng_ancestral/Q03426.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q03426/4_raxmlng_ancestral/Q03426.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q03426/4_raxmlng_ancestral/Q03426.raxml.log

Analysis started: 03-Jun-2021 02:56:37 / finished: 03-Jun-2021 02:56:57

Elapsed time: 20.110 seconds

Consumed energy: 1.259 Wh