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 12-Jul-2021 18:03:42 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/2_msa/Q9UPW6_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/3_mltree/Q9UPW6.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/4_raxmlng_ancestral/Q9UPW6 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626102222
  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/Q9UPW6/2_msa/Q9UPW6_nogap_msa.fasta
[00:00:00] Loaded alignment with 367 taxa and 733 sites

WARNING: Sequences tr_E1BRH4_E1BRH4_CHICK_9031 and tr_A0A087RJY7_A0A087RJY7_APTFO_9233 are exactly identical!
WARNING: Sequences tr_E1BRH4_E1BRH4_CHICK_9031 and tr_A0A0A0AS99_A0A0A0AS99_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_M3XQP5_M3XQP5_MUSPF_9669 and tr_A0A2Y9KBS6_A0A2Y9KBS6_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Y9A7_M3Y9A7_MUSPF_9669 and tr_A0A2U3VFP8_A0A2U3VFP8_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Y9A7_M3Y9A7_MUSPF_9669 and tr_A0A2Y9J046_A0A2Y9J046_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1QJI8_G1QJI8_NOMLE_61853 and tr_A0A2J8U425_A0A2J8U425_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1R5C9_G1R5C9_NOMLE_61853 and tr_H9EQF6_H9EQF6_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1R5C9_G1R5C9_NOMLE_61853 and tr_A0A2K6DWB8_A0A2K6DWB8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I2Z942_A0A2I2Z942_GORGO_9595 and tr_A0A2J8WVE0_A0A2J8WVE0_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2Z942_A0A2I2Z942_GORGO_9595 and tr_A0A2I3SX19_A0A2I3SX19_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2Z942_A0A2I2Z942_GORGO_9595 and sp_Q9UPW6_SATB2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2Z942_A0A2I2Z942_GORGO_9595 and tr_A0A2R9CTC5_A0A2R9CTC5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3QHC8_G3QHC8_GORGO_9595 and tr_A0A2I3S8J9_A0A2I3S8J9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QHC8_G3QHC8_GORGO_9595 and sp_Q01826_SATB1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QHC8_G3QHC8_GORGO_9595 and tr_A0A2R8ZMZ0_A0A2R8ZMZ0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H0YYC4_H0YYC4_TAEGU_59729 and tr_A0A218VDS8_A0A218VDS8_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A096MRX7_A0A096MRX7_PAPAN_9555 and tr_A0A2K5KWR2_A0A2K5KWR2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096MRX7_A0A096MRX7_PAPAN_9555 and tr_A0A2K5ZFE3_A0A2K5ZFE3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3NFQ6_A0A2I3NFQ6_PAPAN_9555 and tr_A0A2K5NDI1_A0A2K5NDI1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3NFQ6_A0A2I3NFQ6_PAPAN_9555 and tr_A0A2K6C8R6_A0A2K6C8R6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3NFQ6_A0A2I3NFQ6_PAPAN_9555 and tr_A0A2K5ZC07_A0A2K5ZC07_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2D0PR33_A0A2D0PR33_ICTPU_7998 and tr_A0A2D0PSN1_A0A2D0PSN1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PR33_A0A2D0PR33_ICTPU_7998 and tr_A0A2D0PSN5_A0A2D0PSN5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PR33_A0A2D0PR33_ICTPU_7998 and tr_A0A2D0PSN9_A0A2D0PSN9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PR33_A0A2D0PR33_ICTPU_7998 and tr_A0A2D0PV95_A0A2D0PV95_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PUD1_A0A2D0PUD1_ICTPU_7998 and tr_W5UIY1_W5UIY1_ICTPU_7998 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/Q9UPW6/4_raxmlng_ancestral/Q9UPW6.raxml.reduced.phy

Alignment comprises 1 partitions and 733 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 733
Gaps: 31.54 %
Invariant sites: 0.27 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/4_raxmlng_ancestral/Q9UPW6.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/Q9UPW6/3_mltree/Q9UPW6.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 184 / 14720
[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: -67955.094831

[00:00:00 -67955.094831] Initial branch length optimization
[00:00:00 -67378.530725] Model parameter optimization (eps = 0.100000)

[00:00:41] Tree #1, final logLikelihood: -66487.295363


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.238107,0.675833) (0.122832,1.685901) (0.355033,0.532710) (0.284028,1.559238) 
   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/Q9UPW6/4_raxmlng_ancestral/Q9UPW6.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/4_raxmlng_ancestral/Q9UPW6.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/4_raxmlng_ancestral/Q9UPW6.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/4_raxmlng_ancestral/Q9UPW6.raxml.log

Analysis started: 12-Jul-2021 18:03:42 / finished: 12-Jul-2021 18:04:26

Elapsed time: 44.457 seconds

Consumed energy: 3.982 Wh