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 01:49:22 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22830/2_msa/P22830_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22830/3_mltree/P22830.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22830/4_raxmlng_ancestral/P22830 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622674162
  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/P22830/2_msa/P22830_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 423 sites

WARNING: Sequences tr_A0A0E1RWL2_A0A0E1RWL2_COCIM_246410 and tr_A0A0J6Y648_A0A0J6Y648_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6Q2C4_B6Q2C4_TALMQ_441960 and tr_A0A093XKD9_A0A093XKD9_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WLB4_B2WLB4_PYRTR_426418 and tr_A0A2W1EQ75_A0A2W1EQ75_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_A0A179UZB3_A0A179UZB3_BLAGS_559298 and tr_C5GXR7_C5GXR7_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_A0A2I3REE8_A0A2I3REE8_PANTR_9598 and tr_A0A2R9A1G4_A0A2R9A1G4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0E0HDC8_A0A0E0HDC8_ORYNI_4536 and sp_A2Y3Q5_HEMH_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0HDC8_A0A0E0HDC8_ORYNI_4536 and tr_I1PUU8_I1PUU8_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0HDC8_A0A0E0HDC8_ORYNI_4536 and tr_A0A0E0PLC9_A0A0E0PLC9_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0HDC8_A0A0E0HDC8_ORYNI_4536 and tr_A0A0D3G6L7_A0A0D3G6L7_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0HDC8_A0A0E0HDC8_ORYNI_4536 and tr_A0A0D9ZY22_A0A0D9ZY22_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0HDC8_A0A0E0HDC8_ORYNI_4536 and sp_Q0DIV0_HEMH2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A2R549_A2R549_ASPNC_425011 and tr_A0A319AF53_A0A319AF53_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XUB1_G7XUB1_ASPKW_1033177 and tr_A0A146FVH9_A0A146FVH9_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F4NRW0_F4NRW0_BATDJ_684364 and tr_A0A177W721_A0A177W721_BATDE_403673 are exactly identical!
WARNING: Sequences tr_I1QMQ7_I1QMQ7_ORYGL_4538 and tr_A0A0E0EQH1_A0A0E0EQH1_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_I1QMQ7_I1QMQ7_ORYGL_4538 and tr_A0A0E0QPC8_A0A0E0QPC8_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1QMQ7_I1QMQ7_ORYGL_4538 and tr_A0A0D3H4V2_A0A0D3H4V2_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1QMQ7_I1QMQ7_ORYGL_4538 and sp_Q69TB1_HEMH1_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G2Y6D3_G2Y6D3_BOTF4_999810 and tr_M7TYM2_M7TYM2_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_A0A3B5XYG5_A0A3B5XYG5_WHEAT_4565 and tr_A0A3B5ZT41_A0A3B5ZT41_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A067EUB0_A0A067EUB0_CITSI_2711 and tr_V4RXN1_V4RXN1_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067GK50_A0A067GK50_CITSI_2711 and tr_A0A2H5PZC2_A0A2H5PZC2_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0A2W8L2_A0A0A2W8L2_BEABA_1245745 and tr_A0A2N6NVA5_A0A2N6NVA5_BEABA_176275 are exactly identical!
WARNING: Sequences tr_X0CT88_X0CT88_FUSOX_1089458 and tr_A0A2H3T9C5_A0A2H3T9C5_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_X0CT88_X0CT88_FUSOX_1089458 and tr_A0A2H3HMH0_A0A2H3HMH0_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A0F0I9C1_A0A0F0I9C1_ASPPU_1403190 and tr_A0A2G7G4C2_A0A2G7G4C2_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A0F8UQ15_A0A0F8UQ15_9EURO_308745 and tr_A0A2T5LU27_A0A2T5LU27_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A1S3YBU7_A0A1S3YBU7_TOBAC_4097 and tr_A0A1U7X393_A0A1U7X393_NICSY_4096 are exactly identical!
WARNING: Duplicate sequences found: 28

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/P22830/4_raxmlng_ancestral/P22830.raxml.reduced.phy

Alignment comprises 1 partitions and 423 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 423
Gaps: 12.65 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22830/4_raxmlng_ancestral/P22830.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/P22830/3_mltree/P22830.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 106 / 8480
[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: -175137.817046

[00:00:00 -175137.817046] Initial branch length optimization
[00:00:01 -174490.137034] Model parameter optimization (eps = 0.100000)

[00:00:49] Tree #1, final logLikelihood: -174017.250323


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.217213,0.221823) (0.210030,0.299164) (0.251481,0.802684) (0.321276,2.138734) 
   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/P22830/4_raxmlng_ancestral/P22830.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22830/4_raxmlng_ancestral/P22830.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22830/4_raxmlng_ancestral/P22830.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22830/4_raxmlng_ancestral/P22830.raxml.log

Analysis started: 03-Jun-2021 01:49:22 / finished: 03-Jun-2021 01:50:17

Elapsed time: 54.276 seconds

Consumed energy: 3.240 Wh