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 03-Jun-2021 02:50:22 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50336/2_msa/P50336_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50336/3_mltree/P50336.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50336/4_raxmlng_ancestral/P50336 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622677822
  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/P50336/2_msa/P50336_nogap_msa.fasta
[00:00:00] Loaded alignment with 679 taxa and 477 sites

WARNING: Sequences tr_J3KIF8_J3KIF8_COCIM_246410 and tr_E9CXC4_E9CXC4_COCPS_443226 are exactly identical!
WARNING: Sequences tr_J3KIF8_J3KIF8_COCIM_246410 and tr_A0A0J6Y072_A0A0J6Y072_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QCD1_B6QCD1_TALMQ_441960 and tr_A0A093V8L0_A0A093V8L0_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_G3RPA7_G3RPA7_GORGO_9595 and tr_A0A2J8J108_A0A2J8J108_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RPA7_G3RPA7_GORGO_9595 and tr_A0A2R9BWH7_A0A2R9BWH7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q2M0W7_Q2M0W7_DROPS_46245 and tr_B4GR01_B4GR01_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B8NNI9_B8NNI9_ASPFN_332952 and tr_Q2UN54_Q2UN54_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_A0A2I3SYH2_A0A2I3SYH2_PANTR_9598 and sp_P50336_PPOX_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A0E0FS02_A0A0E0FS02_ORYNI_4536 and tr_A2WUB8_A2WUB8_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0FS02_A0A0E0FS02_ORYNI_4536 and tr_A0A0D9YDX7_A0A0D9YDX7_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0FS02_A0A0E0FS02_ORYNI_4536 and sp_Q5NAI7_PAO1_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G7XAX6_G7XAX6_ASPKW_1033177 and tr_A0A146F7Z5_A0A146F7Z5_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G3YC40_G3YC40_ASPNA_380704 and tr_A0A319AH98_A0A319AH98_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_M4EAB5_M4EAB5_BRARP_51351 and tr_A0A078GNB9_A0A078GNB9_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4EQK1_M4EQK1_BRARP_51351 and tr_A0A078G8E7_A0A078G8E7_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M0S1J5_M0S1J5_MUSAM_214687 and tr_M0UBQ4_M0UBQ4_MUSAM_214687 are exactly identical!
WARNING: Sequences tr_R1BHN1_R1BHN1_EMIHU_2903 and tr_R1D1P1_R1D1P1_EMIHU_2903 are exactly identical!
WARNING: Sequences tr_V2YA44_V2YA44_MONRO_1381753 and tr_A0A0W0FR84_A0A0W0FR84_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2RGL1_W2RGL1_PHYPN_761204 and tr_A0A0W8BZB6_A0A0W8BZB6_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A015KZ05_A0A015KZ05_9GLOM_1432141 and tr_A0A2I1FZ53_A0A2I1FZ53_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015KZ05_A0A015KZ05_9GLOM_1432141 and tr_U9UWY5_U9UWY5_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A096ML65_A0A096ML65_PAPAN_9555 and tr_A0A2K5LKC9_A0A2K5LKC9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096ML65_A0A096ML65_PAPAN_9555 and tr_A0A2K6EA02_A0A2K6EA02_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096ML65_A0A096ML65_PAPAN_9555 and tr_A0A2K5ZJ67_A0A2K5ZJ67_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3LFF4_A0A2I3LFF4_PAPAN_9555 and tr_A0A0D9S438_A0A0D9S438_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3LFF4_A0A2I3LFF4_PAPAN_9555 and tr_A0A2K5P365_A0A2K5P365_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1S9DYY6_A0A1S9DYY6_ASPOZ_5062 and tr_A0A2G7FLY8_A0A2G7FLY8_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A2P6N623_A0A2P6N623_9MYCE_1890364 and tr_A0A2P6NRB8_A0A2P6NRB8_9MYCE_1890364 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/P50336/4_raxmlng_ancestral/P50336.raxml.reduced.phy

Alignment comprises 1 partitions and 477 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 477
Gaps: 25.37 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50336/4_raxmlng_ancestral/P50336.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/P50336/3_mltree/P50336.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 120 / 9600
[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: -321471.394959

[00:00:00 -321471.394959] Initial branch length optimization
[00:00:01 -273568.112980] Model parameter optimization (eps = 0.100000)

[00:00:54] Tree #1, final logLikelihood: -272162.843574


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.199684,0.533768) (0.168228,0.595448) (0.331142,0.863834) (0.300945,1.685328) 
   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/P50336/4_raxmlng_ancestral/P50336.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50336/4_raxmlng_ancestral/P50336.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50336/4_raxmlng_ancestral/P50336.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50336/4_raxmlng_ancestral/P50336.raxml.log

Analysis started: 03-Jun-2021 02:50:22 / finished: 03-Jun-2021 02:51:20

Elapsed time: 57.665 seconds

Consumed energy: 5.463 Wh