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 01:52:16 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6QNK2/2_msa/Q6QNK2_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6QNK2/3_mltree/Q6QNK2.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6QNK2/4_raxmlng_ancestral/Q6QNK2 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622674336
  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/Q6QNK2/2_msa/Q6QNK2_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 874 sites

WARNING: Sequences sp_Q80TR1_AGRL1_MOUSE_10090 and tr_A0A1U8D2E1_A0A1U8D2E1_MESAU_10036 are exactly identical!
WARNING: Sequences tr_A0A2I3HZQ9_A0A2I3HZQ9_NOMLE_61853 and sp_O94910_AGRL1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3HZQ9_A0A2I3HZQ9_NOMLE_61853 and tr_F7C0V2_F7C0V2_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3HZQ9_A0A2I3HZQ9_NOMLE_61853 and tr_U3FRU9_U3FRU9_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3HZQ9_A0A2I3HZQ9_NOMLE_61853 and tr_A0A0A0MU59_A0A0A0MU59_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3HZQ9_A0A2I3HZQ9_NOMLE_61853 and tr_A0A0D9R202_A0A0D9R202_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3HZQ9_A0A2I3HZQ9_NOMLE_61853 and tr_A0A2K6AUX8_A0A2K6AUX8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3HZQ9_A0A2I3HZQ9_NOMLE_61853 and tr_A0A2K6A057_A0A2K6A057_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2Y9M5_A0A2I2Y9M5_GORGO_9595 and tr_A0A2I3SPU9_A0A2I3SPU9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2Y9M5_A0A2I2Y9M5_GORGO_9595 and tr_A0A2R9BN58_A0A2R9BN58_PANPA_9597 are exactly identical!
WARNING: Sequences tr_E2R3S4_E2R3S4_CANLF_9615 and tr_L5K5D5_L5K5D5_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_A0A2I3SX25_A0A2I3SX25_PANTR_9598 and tr_A0A2R9CMG8_A0A2R9CMG8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5Q5W8_A0A1D5Q5W8_MACMU_9544 and tr_A0A2I3LF52_A0A2I3LF52_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5Q5W8_A0A1D5Q5W8_MACMU_9544 and tr_A0A2K6BMB7_A0A2K6BMB7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6TIA3_F6TIA3_MACMU_9544 and tr_G7P4S5_G7P4S5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A151P2J9_A0A151P2J9_ALLMI_8496 and tr_A0A3Q0FQV3_A0A3Q0FQV3_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0V0ZTY0_A0A0V0ZTY0_9BILA_990121 and tr_A0A0V1P4J1_A0A0V1P4J1_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A2D0QEZ6_A0A2D0QEZ6_ICTPU_7998 and tr_A0A2D0QFZ6_A0A2D0QFZ6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEZ6_A0A2D0QEZ6_ICTPU_7998 and tr_A0A2D0QHD6_A0A2D0QHD6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QHE2_A0A2D0QHE2_ICTPU_7998 and tr_A0A2D0QI94_A0A2D0QI94_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RR99_A0A2D0RR99_ICTPU_7998 and tr_A0A2D0RRB1_A0A2D0RRB1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RRB5_A0A2D0RRB5_ICTPU_7998 and tr_A0A2D0RSV7_A0A2D0RSV7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T4Z7_A0A2D0T4Z7_ICTPU_7998 and tr_A0A2D0T4Z8_A0A2D0T4Z8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T4Z7_A0A2D0T4Z7_ICTPU_7998 and tr_A0A2D0T509_A0A2D0T509_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T4Z7_A0A2D0T4Z7_ICTPU_7998 and tr_A0A2D0T589_A0A2D0T589_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5NIQ2_A0A2K5NIQ2_CERAT_9531 and tr_A0A2K5Y0A0_A0A2K5Y0A0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5NNE1_A0A2K5NNE1_CERAT_9531 and tr_A0A2R8ZME8_A0A2R8ZME8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2Y9LYP0_A0A2Y9LYP0_DELLE_9749 and tr_A0A384A475_A0A384A475_BALAS_310752 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/Q6QNK2/4_raxmlng_ancestral/Q6QNK2.raxml.reduced.phy

Alignment comprises 1 partitions and 874 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 874
Gaps: 32.12 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6QNK2/4_raxmlng_ancestral/Q6QNK2.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/Q6QNK2/3_mltree/Q6QNK2.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 219 / 17520
[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: -369047.203908

[00:00:00 -369047.203908] Initial branch length optimization
[00:00:02 -367717.151252] Model parameter optimization (eps = 0.100000)

[00:01:00] Tree #1, final logLikelihood: -366435.972221


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.110822,0.409274) (0.118349,0.485970) (0.434022,0.850887) (0.336807,1.567144) 
   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/Q6QNK2/4_raxmlng_ancestral/Q6QNK2.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6QNK2/4_raxmlng_ancestral/Q6QNK2.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6QNK2/4_raxmlng_ancestral/Q6QNK2.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6QNK2/4_raxmlng_ancestral/Q6QNK2.raxml.log

Analysis started: 03-Jun-2021 01:52:16 / finished: 03-Jun-2021 01:53:24

Elapsed time: 68.716 seconds

Consumed energy: 3.613 Wh