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 15-Jul-2021 12:54:12 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31327/2_msa/P31327_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31327/3_mltree/P31327.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31327/4_raxmlng_ancestral/P31327 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626342852
  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/P31327/2_msa/P31327_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1500 sites

WARNING: Sequences tr_J3K365_J3K365_COCIM_246410 and tr_A0A0J6Y1X7_A0A0J6Y1X7_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QMA7_B6QMA7_TALMQ_441960 and tr_A0A093XKS0_A0A093XKS0_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B6QNJ3_B6QNJ3_TALMQ_441960 and tr_A0A093UY59_A0A093UY59_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WG47_B2WG47_PYRTR_426418 and tr_A0A2W1H0M7_A0A2W1H0M7_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_B8NB80_B8NB80_ASPFN_332952 and tr_Q2U015_Q2U015_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NB80_B8NB80_ASPFN_332952 and tr_A0A1S9DD88_A0A1S9DD88_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UFA5_A0A179UFA5_BLAGS_559298 and tr_C5GJ72_C5GJ72_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9G3E4_F9G3E4_FUSOF_660025 and tr_X0CS33_X0CS33_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A2QRW1_A2QRW1_ASPNC_425011 and tr_A0A318ZWA8_A0A318ZWA8_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XKD1_G7XKD1_ASPKW_1033177 and tr_A0A146FTG3_A0A146FTG3_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G2XYH0_G2XYH0_BOTF4_999810 and tr_M7TR11_M7TR11_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SIW5_F2SIW5_TRIRC_559305 and tr_A0A178F3C8_A0A178F3C8_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_B3S4V3_B3S4V3_TRIAD_10228 and tr_A0A369RTC8_A0A369RTC8_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G3Y662_G3Y662_ASPNA_380704 and tr_A0A319APN5_A0A319APN5_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_N4UUK1_N4UUK1_FUSC1_1229664 and tr_A0A2H3T979_A0A2H3T979_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_N4UUK1_N4UUK1_FUSC1_1229664 and tr_A0A2H3HZ76_A0A2H3HZ76_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_V2XQV9_V2XQV9_MONRO_1381753 and tr_A0A0W0F1Z5_A0A0W0F1Z5_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A096MNE6_A0A096MNE6_PAPAN_9555 and tr_A0A2K5YJ64_A0A2K5YJ64_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A094ELU0_A0A094ELU0_9PEZI_1420912 and tr_A0A1B8GIH2_A0A1B8GIH2_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0F8V0B7_A0A0F8V0B7_9EURO_308745 and tr_A0A2T5M3U9_A0A2T5M3U9_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A100IL89_A0A100IL89_ASPNG_5061 and tr_A0A1L9N3R7_A0A1L9N3R7_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A124BXC6_A0A124BXC6_ASPNG_5061 and tr_A0A1L9NPV8_A0A1L9NPV8_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A164WS13_A0A164WS13_9HOMO_1314777 and tr_A0A166DD29_A0A166DD29_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1Q3E9N9_A0A1Q3E9N9_LENED_5353 and tr_A0A1Q3EA11_A0A1Q3EA11_LENED_5353 are exactly identical!
WARNING: Sequences tr_A0A2N5SH46_A0A2N5SH46_9BASI_200324 and tr_A0A2N5T335_A0A2N5T335_9BASI_200324 are exactly identical!
WARNING: Sequences tr_A0A2V5IY94_A0A2V5IY94_9EURO_1450541 and tr_A0A2V5HKL0_A0A2V5HKL0_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 26

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/P31327/4_raxmlng_ancestral/P31327.raxml.reduced.phy

Alignment comprises 1 partitions and 1500 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 1500
Gaps: 7.99 %
Invariant sites: 7.33 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31327/4_raxmlng_ancestral/P31327.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/P31327/3_mltree/P31327.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 375 / 30000
[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: -438557.334423

[00:00:00 -438557.334423] Initial branch length optimization
[00:00:03 -433237.949753] Model parameter optimization (eps = 0.100000)

[00:01:03] Tree #1, final logLikelihood: -432126.568216


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.302163,0.260688) (0.299965,0.433863) (0.228238,1.157956) (0.169635,3.105481) 
   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/P31327/4_raxmlng_ancestral/P31327.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31327/4_raxmlng_ancestral/P31327.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31327/4_raxmlng_ancestral/P31327.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31327/4_raxmlng_ancestral/P31327.raxml.log

Analysis started: 15-Jul-2021 12:54:12 / finished: 15-Jul-2021 12:55:30

Elapsed time: 78.290 seconds

Consumed energy: 5.948 Wh