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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 02-Jun-2021 17:53:09 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O15269/2_msa/O15269_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O15269/3_mltree/O15269.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O15269/4_raxmlng_ancestral/O15269 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622645589
  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/O15269/2_msa/O15269_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 473 sites

WARNING: Sequences tr_B2W8K3_B2W8K3_PYRTR_426418 and tr_A0A2W1DDY7_A0A2W1DDY7_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_B8NS48_B8NS48_ASPFN_332952 and tr_A0A0F0I998_A0A0F0I998_ASPPU_1403190 are exactly identical!
WARNING: Sequences tr_B8NS48_B8NS48_ASPFN_332952 and tr_A0A1S9D6C4_A0A1S9D6C4_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179U8L2_A0A179U8L2_BLAGS_559298 and tr_C5GVQ2_C5GVQ2_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9FCG7_F9FCG7_FUSOF_660025 and tr_A0A0D2XIG8_A0A0D2XIG8_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FCG7_F9FCG7_FUSOF_660025 and tr_N4TQM9_N4TQM9_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FCG7_F9FCG7_FUSOF_660025 and tr_X0CTR2_X0CTR2_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FCG7_F9FCG7_FUSOF_660025 and tr_A0A2H3TJ20_A0A2H3TJ20_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FCG7_F9FCG7_FUSOF_660025 and tr_A0A2H3HG19_A0A2H3HG19_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_E9EWQ8_E9EWQ8_METRA_655844 and tr_A0A0D9PDD3_A0A0D9PDD3_METAN_1291518 are exactly identical!
WARNING: Sequences tr_A0A0E0H7L8_A0A0E0H7L8_ORYNI_4536 and tr_A0A0E0B8J6_A0A0E0B8J6_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A2QLK3_A2QLK3_ASPNC_425011 and tr_G3YFY0_G3YFY0_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QLK3_A2QLK3_ASPNC_425011 and tr_A0A318ZYP1_A0A318ZYP1_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_H9FNT1_H9FNT1_MACMU_9544 and tr_A0A2K5ZWP1_A0A2K5ZWP1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7XM26_G7XM26_ASPKW_1033177 and tr_A0A146F972_A0A146F972_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A2XAS3_A2XAS3_ORYSI_39946 and tr_A0A0E0NMI1_A0A0E0NMI1_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A2XEM2_A2XEM2_ORYSI_39946 and tr_A0A0E0NSJ6_A0A0E0NSJ6_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A2XEM2_A2XEM2_ORYSI_39946 and sp_Q10P01_LCB1A_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1P5C7_I1P5C7_ORYGL_4538 and tr_A0A0D3FBT9_A0A0D3FBT9_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1QT45_I1QT45_ORYGL_4538 and tr_A0A0D3HBW6_A0A0D3HBW6_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_R7R239_R7R239_BOTF4_999810 and tr_M7TR35_M7TR35_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_L2FEV7_L2FEV7_COLFN_1213859 and tr_T0LJA3_T0LJA3_COLGC_1237896 are exactly identical!
WARNING: Sequences tr_S2IY89_S2IY89_MUCC1_1220926 and tr_A0A0C9MM87_A0A0C9MM87_9FUNG_91626 are exactly identical!
WARNING: Sequences tr_A0A015J5Y8_A0A015J5Y8_9GLOM_1432141 and tr_U9UNH3_U9UNH3_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2I3MPL3_A0A2I3MPL3_PAPAN_9555 and tr_A0A2K6B033_A0A2K6B033_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0F8XCK7_A0A0F8XCK7_9EURO_308745 and tr_A0A2T5LPF9_A0A2T5LPF9_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A117E290_A0A117E290_ASPNG_5061 and tr_A0A317UTP8_A0A317UTP8_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A0A166W7Q8_A0A166W7Q8_9PEZI_708197 and tr_A0A161YCU2_A0A161YCU2_9PEZI_1573173 are exactly identical!
WARNING: Sequences tr_A0A164YHI0_A0A164YHI0_9HOMO_1314777 and tr_A0A166I336_A0A166I336_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S4CVC1_A0A1S4CVC1_TOBAC_4097 and tr_A0A1U7UMI5_A0A1U7UMI5_NICSY_4096 are exactly identical!
WARNING: Duplicate sequences found: 30

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/O15269/4_raxmlng_ancestral/O15269.raxml.reduced.phy

Alignment comprises 1 partitions and 473 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 473
Gaps: 8.20 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O15269/4_raxmlng_ancestral/O15269.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/O15269/3_mltree/O15269.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: -239286.683345

[00:00:00 -239286.683345] Initial branch length optimization
[00:00:01 -238696.367621] Model parameter optimization (eps = 0.100000)

[00:00:30] Tree #1, final logLikelihood: -238026.075309


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.180256,0.434832) (0.307153,0.522763) (0.277961,1.012001) (0.234630,2.044725) 
   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/O15269/4_raxmlng_ancestral/O15269.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O15269/4_raxmlng_ancestral/O15269.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O15269/4_raxmlng_ancestral/O15269.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O15269/4_raxmlng_ancestral/O15269.raxml.log

Analysis started: 02-Jun-2021 17:53:09 / finished: 02-Jun-2021 17:53:44

Elapsed time: 35.307 seconds

Consumed energy: 2.863 Wh