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 02:37:47 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43272/2_msa/O43272_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43272/3_mltree/O43272.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43272/4_raxmlng_ancestral/O43272 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622677067
  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/O43272/2_msa/O43272_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 600 sites

WARNING: Sequences tr_H2QG46_H2QG46_PANTR_9598 and tr_A0A2R9AAY8_A0A2R9AAY8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FTM3_F9FTM3_FUSOF_660025 and tr_X0CMX6_X0CMX6_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FTM3_F9FTM3_FUSOF_660025 and tr_A0A2H3T3V2_A0A2H3T3V2_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FTM3_F9FTM3_FUSOF_660025 and tr_A0A2H3FWE5_A0A2H3FWE5_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_F9G300_F9G300_FUSOF_660025 and tr_A0A0D2XP52_A0A0D2XP52_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9G300_F9G300_FUSOF_660025 and tr_N4U0N5_N4U0N5_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9G300_F9G300_FUSOF_660025 and tr_X0BT11_X0BT11_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9G300_F9G300_FUSOF_660025 and tr_A0A2H3TRP7_A0A2H3TRP7_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9G300_F9G300_FUSOF_660025 and tr_A0A2H3HMB8_A0A2H3HMB8_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_F9G300_F9G300_FUSOF_660025 and tr_A0A365NE94_A0A365NE94_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_E9F9P4_E9F9P4_METRA_655844 and tr_A0A0B4HNZ5_A0A0B4HNZ5_METMF_1276143 are exactly identical!
WARNING: Sequences tr_J4KQY4_J4KQY4_BEAB2_655819 and tr_A0A0A2VXP4_A0A0A2VXP4_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_Q2UN06_Q2UN06_ASPOR_510516 and tr_A0A1S9D6E3_A0A1S9D6E3_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_Q2UTG0_Q2UTG0_ASPOR_510516 and tr_A0A1S9DXH2_A0A1S9DXH2_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A2Q7Q2_A2Q7Q2_ASPNC_425011 and tr_A0A318ZXP0_A0A318ZXP0_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A2QNB4_A2QNB4_ASPNC_425011 and tr_A0A319ABJ7_A0A319ABJ7_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XF58_G7XF58_ASPKW_1033177 and tr_A0A146F0Y5_A0A146F0Y5_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XL11_G7XL11_ASPKW_1033177 and tr_A0A146EXV8_A0A146EXV8_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XXY5_G7XXY5_ASPKW_1033177 and tr_A0A146FPB6_A0A146FPB6_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A2ZA15_A2ZA15_ORYSI_39946 and tr_A0A0E0R288_A0A0E0R288_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A2ZA15_A2ZA15_ORYSI_39946 and tr_Q336U3_Q336U3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F2T0J7_F2T0J7_TRIRC_559305 and tr_A0A178F7Y7_A0A178F7Y7_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_W7M9B3_W7M9B3_GIBM7_334819 and tr_A0A2K0WUX1_A0A2K0WUX1_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_F2Q594_F2Q594_TRIEC_559882 and tr_A0A059JJE7_A0A059JJE7_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_W2RJ79_W2RJ79_PHYPN_761204 and tr_W2JUN6_W2JUN6_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A067EUQ2_A0A067EUQ2_CITSI_2711 and tr_A0A2H5P2B7_A0A2H5P2B7_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A078HDI3_A0A078HDI3_BRANA_3708 and tr_A0A0D3AWR1_A0A0D3AWR1_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A1S3ZT73_A0A1S3ZT73_TOBAC_4097 and tr_A0A1U7V9S1_A0A1U7V9S1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_Q8W415_Q8W415_TOBAC_4097 and tr_A0A1U7Y6V2_A0A1U7Y6V2_NICSY_4096 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/O43272/4_raxmlng_ancestral/O43272.raxml.reduced.phy

Alignment comprises 1 partitions and 600 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 600
Gaps: 29.15 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43272/4_raxmlng_ancestral/O43272.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/O43272/3_mltree/O43272.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 150 / 12000
[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: -305837.490297

[00:00:00 -305837.490297] Initial branch length optimization
[00:00:01 -304920.264416] Model parameter optimization (eps = 0.100000)

[00:00:38] Tree #1, final logLikelihood: -304170.344848


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.133240,0.325575) (0.182533,0.341251) (0.335229,0.857009) (0.348998,1.739371) 
   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/O43272/4_raxmlng_ancestral/O43272.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43272/4_raxmlng_ancestral/O43272.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43272/4_raxmlng_ancestral/O43272.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43272/4_raxmlng_ancestral/O43272.raxml.log

Analysis started: 03-Jun-2021 02:37:47 / finished: 03-Jun-2021 02:38:31

Elapsed time: 44.228 seconds

Consumed energy: 3.172 Wh