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 02:32:31 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBM7/2_msa/Q9UBM7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBM7/3_mltree/Q9UBM7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBM7/4_raxmlng_ancestral/Q9UBM7 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622676751
  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/Q9UBM7/2_msa/Q9UBM7_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 475 sites

WARNING: Sequences tr_B6Q6F5_B6Q6F5_TALMQ_441960 and tr_A0A093XZX5_A0A093XZX5_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_C0NUB7_C0NUB7_AJECG_447093 and tr_C6H1R9_C6H1R9_AJECH_544712 are exactly identical!
WARNING: Sequences tr_H2R2E7_H2R2E7_PANTR_9598 and tr_A0A2R9BUA6_A0A2R9BUA6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9G0E7_F9G0E7_FUSOF_660025 and tr_X0C342_X0C342_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9G0E7_F9G0E7_FUSOF_660025 and tr_A0A2K0WJ99_A0A2K0WJ99_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_C6HL79_C6HL79_AJECH_544712 and tr_F0UEB9_F0UEB9_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A0E0IBC0_A0A0E0IBC0_ORYNI_4536 and tr_A0A0E0NEL4_A0A0E0NEL4_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_F7EBC6_F7EBC6_MACMU_9544 and tr_G7NTV9_G7NTV9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7EBC6_F7EBC6_MACMU_9544 and tr_A0A2K6ARY8_A0A2K6ARY8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G2YH65_G2YH65_BOTF4_999810 and tr_M7TN49_M7TN49_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SBL5_F2SBL5_TRIRC_559305 and tr_A0A178ETN8_A0A178ETN8_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_A0A0D2YJ64_A0A0D2YJ64_FUSO4_426428 and tr_N4UDN2_N4UDN2_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_A0A0D2YJ64_A0A0D2YJ64_FUSO4_426428 and tr_X0BWD3_X0BWD3_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0D2YJ64_A0A0D2YJ64_FUSO4_426428 and tr_A0A2H3GLE0_A0A2H3GLE0_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_M4DCN6_M4DCN6_BRARP_51351 and tr_A0A078I5B1_A0A078I5B1_BRANA_3708 are exactly identical!
WARNING: Sequences tr_V2X877_V2X877_MONRO_1381753 and tr_A0A0W0FIY8_A0A0W0FIY8_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_V2XLQ7_V2XLQ7_MONRO_1381753 and tr_A0A0W0EXQ6_A0A0W0EXQ6_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_V2Y1S2_V2Y1S2_MONRO_1381753 and tr_A0A0W0FJF2_A0A0W0FJF2_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2Q7H3_W2Q7H3_PHYPN_761204 and tr_W2NBL2_W2NBL2_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015KGI1_A0A015KGI1_9GLOM_1432141 and tr_U9SFU0_U9SFU0_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015LJR1_A0A015LJR1_9GLOM_1432141 and tr_A0A2H5TNV7_A0A2H5TNV7_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A1S3XXK7_A0A1S3XXK7_TOBAC_4097 and tr_A0A1U7YK08_A0A1U7YK08_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2K5KHK1_A0A2K5KHK1_CERAT_9531 and tr_A0A2K6CT75_A0A2K6CT75_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2K5KHK1_A0A2K5KHK1_CERAT_9531 and tr_A0A2K5ZRW8_A0A2K5ZRW8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U3V778_A0A2U3V778_TURTR_9739 and tr_A0A2U4AUP7_A0A2U4AUP7_TURTR_9739 are exactly identical!
WARNING: Duplicate sequences found: 25

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/Q9UBM7/4_raxmlng_ancestral/Q9UBM7.raxml.reduced.phy

Alignment comprises 1 partitions and 475 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 475
Gaps: 15.43 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBM7/4_raxmlng_ancestral/Q9UBM7.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/Q9UBM7/3_mltree/Q9UBM7.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 119 / 9520
[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: -245939.375612

[00:00:00 -245939.375612] Initial branch length optimization
[00:00:01 -244866.663612] Model parameter optimization (eps = 0.100000)

[00:00:33] Tree #1, final logLikelihood: -243892.107008


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.147063,0.377748) (0.326195,0.522876) (0.367155,1.209560) (0.159586,2.066541) 
   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/Q9UBM7/4_raxmlng_ancestral/Q9UBM7.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBM7/4_raxmlng_ancestral/Q9UBM7.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBM7/4_raxmlng_ancestral/Q9UBM7.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBM7/4_raxmlng_ancestral/Q9UBM7.raxml.log

Analysis started: 03-Jun-2021 02:32:31 / finished: 03-Jun-2021 02:33:09

Elapsed time: 37.765 seconds

Consumed energy: 2.257 Wh