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 02:00:38 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P82251/2_msa/P82251_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P82251/3_mltree/P82251.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P82251/4_raxmlng_ancestral/P82251 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622674838
  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/P82251/2_msa/P82251_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 487 sites

WARNING: Sequences tr_Q9Y1A7_Q9Y1A7_DROME_7227 and tr_B4HHV5_B4HHV5_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A2I2ZD48_A0A2I2ZD48_GORGO_9595 and tr_H2QBE0_H2QBE0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2ZD48_A0A2I2ZD48_GORGO_9595 and sp_Q92536_YLAT2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QM98_G3QM98_GORGO_9595 and tr_H2Q7Z2_H2Q7Z2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QM98_G3QM98_GORGO_9595 and sp_Q9UM01_YLAT1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QWU8_G3QWU8_GORGO_9595 and tr_H2NKS2_H2NKS2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QWU8_G3QWU8_GORGO_9595 and sp_Q5RAE3_LAT2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QWU8_G3QWU8_GORGO_9595 and tr_A0A2I3TPJ3_A0A2I3TPJ3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QWU8_G3QWU8_GORGO_9595 and sp_Q9UHI5_LAT2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QWU8_G3QWU8_GORGO_9595 and tr_A0A2R9A4Y1_A0A2R9A4Y1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3SDE4_G3SDE4_GORGO_9595 and sp_Q9UPY5_XCT_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_Q29NJ9_Q29NJ9_DROPS_46245 and tr_B4GQJ3_B4GQJ3_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A2I3RTW4_A0A2I3RTW4_PANTR_9598 and tr_A0A2R9BUE9_A0A2R9BUE9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2J8KSU5_A0A2J8KSU5_PANTR_9598 and tr_A0A2R9C2F7_A0A2R9C2F7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0J9Y4Y3_A0A0J9Y4Y3_BRUMA_6279 and tr_A0A0N4T1E9_A0A0N4T1E9_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_A0A0J9Y4Y3_A0A0J9Y4Y3_BRUMA_6279 and tr_A0A0R3QQU3_A0A0R3QQU3_9BILA_42155 are exactly identical!
WARNING: Sequences tr_F6WP35_F6WP35_MACMU_9544 and tr_G7P6A5_G7P6A5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6WP35_F6WP35_MACMU_9544 and tr_A0A0D9S0W4_A0A0D9S0W4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6WP35_F6WP35_MACMU_9544 and tr_A0A2K6A3I1_A0A2K6A3I1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6XDS9_F6XDS9_MACMU_9544 and tr_G7PX58_G7PX58_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7CUI1_F7CUI1_MACMU_9544 and tr_G7P9V4_G7P9V4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7CUI1_F7CUI1_MACMU_9544 and tr_A0A2K6DE56_A0A2K6DE56_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7MX23_G7MX23_MACMU_9544 and tr_A0A2K6E1G5_A0A2K6E1G5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7Q1G5_G7Q1G5_MACFA_9541 and tr_A0A096NFR2_A0A096NFR2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7Q1G5_G7Q1G5_MACFA_9541 and tr_A0A2K5MYG1_A0A2K5MYG1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7Q1G5_G7Q1G5_MACFA_9541 and tr_A0A2K6BIB3_A0A2K6BIB3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NG78_A0A096NG78_PAPAN_9555 and tr_A0A2K6C916_A0A2K6C916_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0A0MW31_A0A0A0MW31_PAPAN_9555 and tr_A0A2K5LYA5_A0A2K5LYA5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A151MM22_A0A151MM22_ALLMI_8496 and tr_A0A1U8CVV7_A0A1U8CVV7_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A1S3MM81_A0A1S3MM81_SALSA_8030 and tr_A0A060VXC5_A0A060VXC5_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A2U4CF75_A0A2U4CF75_TURTR_9739 and tr_A0A2U4CF76_A0A2U4CF76_TURTR_9739 are exactly identical!
WARNING: Duplicate sequences found: 31

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/P82251/4_raxmlng_ancestral/P82251.raxml.reduced.phy

Alignment comprises 1 partitions and 487 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 487
Gaps: 4.64 %
Invariant sites: 0.82 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P82251/4_raxmlng_ancestral/P82251.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/P82251/3_mltree/P82251.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 122 / 9760
[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: -205821.701277

[00:00:00 -205821.701277] Initial branch length optimization
[00:00:01 -204454.621168] Model parameter optimization (eps = 0.100000)

[00:00:30] Tree #1, final logLikelihood: -203415.567691


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.300630,0.452027) (0.327835,0.589203) (0.255840,1.301978) (0.115694,2.920169) 
   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/P82251/4_raxmlng_ancestral/P82251.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P82251/4_raxmlng_ancestral/P82251.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P82251/4_raxmlng_ancestral/P82251.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P82251/4_raxmlng_ancestral/P82251.raxml.log

Analysis started: 03-Jun-2021 02:00:38 / finished: 03-Jun-2021 02:01:13

Elapsed time: 34.890 seconds

Consumed energy: 2.441 Wh