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 02:04:03 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P21333/2_msa/P21333_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P21333/3_mltree/P21333.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P21333/4_raxmlng_ancestral/P21333 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622675043
  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/P21333/2_msa/P21333_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 2647 sites

WARNING: Sequences sp_Q9JI91_ACTN2_MOUSE_10090 and tr_D3ZCV0_D3ZCV0_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3Y7F4_M3Y7F4_MUSPF_9669 and tr_A0A2Y9JK69_A0A2Y9JK69_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A0D8JUP7_A0A0D8JUP7_COCIM_246410 and tr_E9DI27_E9DI27_COCPS_443226 are exactly identical!
WARNING: Sequences tr_A0A0D8JUP7_A0A0D8JUP7_COCIM_246410 and tr_A0A0J6Y5M8_A0A0J6Y5M8_COCIT_404692 are exactly identical!
WARNING: Sequences tr_E2QY08_E2QY08_CANLF_9615 and tr_A0A2U3ZCZ8_A0A2U3ZCZ8_ODORO_9708 are exactly identical!
WARNING: Sequences tr_A0A2I3STF2_A0A2I3STF2_PANTR_9598 and tr_A0A0A0MU58_A0A0A0MU58_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3STF2_A0A2I3STF2_PANTR_9598 and tr_A0A2K5LF87_A0A2K5LF87_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3STF2_A0A2I3STF2_PANTR_9598 and tr_A0A2R9C199_A0A2R9C199_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7CD41_K7CD41_PANTR_9598 and tr_A0A2R9AD40_A0A2R9AD40_PANPA_9597 are exactly identical!
WARNING: Sequences tr_E9F107_E9F107_METRA_655844 and tr_A0A0B4IDV1_A0A0B4IDV1_METMF_1276143 are exactly identical!
WARNING: Sequences tr_E9F107_E9F107_METRA_655844 and tr_A0A0D9NTW3_A0A0D9NTW3_METAN_1291518 are exactly identical!
WARNING: Sequences sp_O43707_ACTN4_HUMAN_9606 and tr_F7HU82_F7HU82_MACMU_9544 are exactly identical!
WARNING: Sequences sp_O43707_ACTN4_HUMAN_9606 and tr_A0A0D9QVJ0_A0A0D9QVJ0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A0D9RKZ5_A0A0D9RKZ5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A2K5N6P5_A0A2K5N6P5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A2K6CYT7_A0A2K6CYT7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A2K5ZZ84_A0A2K5ZZ84_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7PAK8_G7PAK8_MACFA_9541 and tr_A0A2I3MK21_A0A2I3MK21_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_L2FW06_L2FW06_COLFN_1213859 and tr_T0LZM9_T0LZM9_COLGC_1237896 are exactly identical!
WARNING: Sequences tr_A0A2I2UNZ9_A0A2I2UNZ9_FELCA_9685 and tr_A0A384AAW7_A0A384AAW7_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A059IXW0_A0A059IXW0_9EURO_1215338 and tr_A0A178F4W9_A0A178F4W9_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_A0A0D9RBH8_A0A0D9RBH8_CHLSB_60711 and tr_A0A2K6E8I1_A0A2K6E8I1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0D9RC89_A0A0D9RC89_CHLSB_60711 and tr_A0A2K6A9D6_A0A2K6A9D6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A091JKQ5_A0A091JKQ5_EGRGA_188379 and tr_A0A091UMG4_A0A091UMG4_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JKQ5_A0A091JKQ5_EGRGA_188379 and tr_A0A087R6Z3_A0A087R6Z3_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091JKQ5_A0A091JKQ5_EGRGA_188379 and tr_A0A0A0AHU9_A0A0A0AHU9_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0MTN9_A0A2I0MTN9_COLLI_8932 and tr_A0A1V4JKI3_A0A1V4JKI3_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A2U3WWF0_A0A2U3WWF0_ODORO_9708 and tr_A0A2U3Y3N1_A0A2U3Y3N1_LEPWE_9713 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/P21333/4_raxmlng_ancestral/P21333.raxml.reduced.phy

Alignment comprises 1 partitions and 2647 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 2647
Gaps: 53.08 %
Invariant sites: 0.11 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P21333/4_raxmlng_ancestral/P21333.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/P21333/3_mltree/P21333.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 662 / 52960
[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: -534593.944428

[00:00:00 -534593.944428] Initial branch length optimization
[00:00:06 -514641.271308] Model parameter optimization (eps = 0.100000)

[00:03:07] Tree #1, final logLikelihood: -512429.806727


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.177690,0.533658) (0.145406,0.632097) (0.395507,0.796028) (0.281397,1.771266) 
   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/P21333/4_raxmlng_ancestral/P21333.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P21333/4_raxmlng_ancestral/P21333.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P21333/4_raxmlng_ancestral/P21333.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P21333/4_raxmlng_ancestral/P21333.raxml.log

Analysis started: 03-Jun-2021 02:04:03 / finished: 03-Jun-2021 02:07:36

Elapsed time: 212.841 seconds

Consumed energy: 10.766 Wh