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 12-Jul-2021 17:58:46 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/2_msa/P30038_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/3_mltree/P30038.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/4_raxmlng_ancestral/P30038 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626101926
  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/300621_run/phylogeny-snakemake/results/P30038/2_msa/P30038_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 563 sites

WARNING: Sequences tr_A0A0E1RWZ4_A0A0E1RWZ4_COCIM_246410 and tr_A0A0J7B2T2_A0A0J7B2T2_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QB17_B6QB17_TALMQ_441960 and tr_A0A093UVB4_A0A093UVB4_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B8NP70_B8NP70_ASPFN_332952 and tr_Q2UN07_Q2UN07_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_F9FQM3_F9FQM3_FUSOF_660025 and tr_A0A0D2X8P0_A0A0D2X8P0_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FQM3_F9FQM3_FUSOF_660025 and tr_N4TT09_N4TT09_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FQM3_F9FQM3_FUSOF_660025 and tr_X0CFF6_X0CFF6_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FQM3_F9FQM3_FUSOF_660025 and tr_A0A2H3STU9_A0A2H3STU9_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FQM3_F9FQM3_FUSOF_660025 and tr_A0A2H3HUB0_A0A2H3HUB0_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_F9FTM0_F9FTM0_FUSOF_660025 and tr_N4UJG1_N4UJG1_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FTM0_F9FTM0_FUSOF_660025 and tr_X0BYA3_X0BYA3_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FTM0_F9FTM0_FUSOF_660025 and tr_A0A2H3SIW2_A0A2H3SIW2_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FTM0_F9FTM0_FUSOF_660025 and tr_A0A2H3G6B6_A0A2H3G6B6_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_J5K4S2_J5K4S2_BEAB2_655819 and tr_A0A2N6P121_A0A2N6P121_BEABA_176275 are exactly identical!
WARNING: Sequences tr_A0A0J9Y7J2_A0A0J9Y7J2_BRUMA_6279 and tr_A0A0R3QLA3_A0A0R3QLA3_9BILA_42155 are exactly identical!
WARNING: Sequences tr_A2QC50_A2QC50_ASPNC_425011 and tr_A0A319ASJ8_A0A319ASJ8_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A2QNB0_A2QNB0_ASPNC_425011 and tr_G3XYQ8_G3XYQ8_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QNB0_A2QNB0_ASPNC_425011 and tr_A0A319AYY5_A0A319AYY5_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A2QWR5_A2QWR5_ASPNC_425011 and tr_G3YD59_G3YD59_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QWR5_A2QWR5_ASPNC_425011 and tr_A0A319AFZ5_A0A319AFZ5_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7X9Z4_G7X9Z4_ASPKW_1033177 and tr_A0A146F9A7_A0A146F9A7_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XF54_G7XF54_ASPKW_1033177 and tr_A0A146F0T3_A0A146F0T3_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XL12_G7XL12_ASPKW_1033177 and tr_A0A146EXQ3_A0A146EXQ3_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F9WYJ2_F9WYJ2_ZYMTI_336722 and tr_A0A1X7RHA3_A0A1X7RHA3_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_F2SZD4_F2SZD4_TRIRC_559305 and tr_A0A178F3X5_A0A178F3X5_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_F2Q593_F2Q593_TRIEC_559882 and tr_A0A059J012_A0A059J012_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_U5HJ93_U5HJ93_USTV1_683840 and tr_A0A2X0M9R4_A0A2X0M9R4_9BASI_796604 are exactly identical!
WARNING: Sequences tr_A0A0V1D926_A0A0V1D926_TRIBR_45882 and tr_A0A0V1NIR6_A0A0V1NIR6_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A100IDU6_A0A100IDU6_ASPNG_5061 and tr_A0A1L9MY83_A0A1L9MY83_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A124BXH6_A0A124BXH6_ASPNG_5061 and tr_A0A1L9N1M9_A0A1L9N1M9_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A124BXH6_A0A124BXH6_ASPNG_5061 and tr_A0A317WEC1_A0A317WEC1_9EURO_1448314 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/300621_run/phylogeny-snakemake/results/P30038/4_raxmlng_ancestral/P30038.raxml.reduced.phy

Alignment comprises 1 partitions and 563 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 563
Gaps: 4.79 %
Invariant sites: 1.24 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/4_raxmlng_ancestral/P30038.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/300621_run/phylogeny-snakemake/results/P30038/3_mltree/P30038.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 141 / 11280
[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: -247003.950315

[00:00:00 -247003.950315] Initial branch length optimization
[00:00:01 -246737.430795] Model parameter optimization (eps = 0.100000)

[00:00:30] Tree #1, final logLikelihood: -246257.342278


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.222114,0.279798) (0.323032,0.460653) (0.213819,0.966622) (0.241036,2.416092) 
   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/300621_run/phylogeny-snakemake/results/P30038/4_raxmlng_ancestral/P30038.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/4_raxmlng_ancestral/P30038.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/4_raxmlng_ancestral/P30038.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/4_raxmlng_ancestral/P30038.raxml.log

Analysis started: 12-Jul-2021 17:58:46 / finished: 12-Jul-2021 17:59:22

Elapsed time: 35.711 seconds

Consumed energy: 2.285 Wh