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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 02-Jun-2021 15:20:26 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24530/2_msa/P24530_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24530/3_mltree/P24530.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24530/4_raxmlng_ancestral/P24530 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622636426
  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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24530/2_msa/P24530_nogap_msa.fasta
[00:00:00] Loaded alignment with 704 taxa and 442 sites

WARNING: Sequences tr_B4QBB3_B4QBB3_DROSI_7240 and tr_B4HMY2_B4HMY2_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B4QCR2_B4QCR2_DROSI_7240 and tr_B4II33_B4II33_DROSE_7238 are exactly identical!
WARNING: Sequences tr_G3QL90_G3QL90_GORGO_9595 and tr_H2PWX4_H2PWX4_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QL90_G3QL90_GORGO_9595 and tr_H2QZ61_H2QZ61_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QL90_G3QL90_GORGO_9595 and sp_P32247_BRS3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QL90_G3QL90_GORGO_9595 and tr_A0A2R9AGX3_A0A2R9AGX3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RL33_G3RL33_GORGO_9595 and tr_H2QYC3_H2QYC3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RL33_G3RL33_GORGO_9595 and tr_A0A2R9B7E7_A0A2R9B7E7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q28WQ5_Q28WQ5_DROPS_46245 and tr_B4H738_B4H738_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q28Z40_Q28Z40_DROPS_46245 and tr_B4GIB2_B4GIB2_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2Q7N9_H2Q7N9_PANTR_9598 and sp_P24530_EDNRB_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q7N9_H2Q7N9_PANTR_9598 and tr_A0A2R8ZUY0_A0A2R8ZUY0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QQ94_H2QQ94_PANTR_9598 and sp_P25101_EDNRA_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F7HCY5_F7HCY5_MACMU_9544 and tr_G7Q2A5_G7Q2A5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7HCY5_F7HCY5_MACMU_9544 and tr_A0A096N446_A0A096N446_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7HCY5_F7HCY5_MACMU_9544 and tr_A0A0D9RQR5_A0A0D9RQR5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7HCY5_F7HCY5_MACMU_9544 and tr_A0A2K5MF51_A0A2K5MF51_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7HCY5_F7HCY5_MACMU_9544 and tr_A0A2K6B9L2_A0A2K6B9L2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HCY5_F7HCY5_MACMU_9544 and tr_A0A2K5YY89_A0A2K5YY89_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7P315_G7P315_MACFA_9541 and tr_A0A2K6DGY1_A0A2K6DGY1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7P315_G7P315_MACFA_9541 and tr_A0A2K5XDB6_A0A2K5XDB6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7P6D6_G7P6D6_MACFA_9541 and tr_A0A2K6AN52_A0A2K6AN52_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096N1F9_A0A096N1F9_PAPAN_9555 and tr_A0A2K5M4R7_A0A2K5M4R7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096N1F9_A0A096N1F9_PAPAN_9555 and tr_A0A2K5YWQ0_A0A2K5YWQ0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096N1H2_A0A096N1H2_PAPAN_9555 and tr_A0A2K5NLW6_A0A2K5NLW6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A226NDD6_A0A226NDD6_CALSU_9009 and tr_A0A226PLI1_A0A226PLI1_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2K5LET3_A0A2K5LET3_CERAT_9531 and tr_A0A2K6AXZ8_A0A2K6AXZ8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2K5LET3_A0A2K5LET3_CERAT_9531 and tr_A0A2K5YGA7_A0A2K5YGA7_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 28

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24530/4_raxmlng_ancestral/P24530.raxml.reduced.phy

Alignment comprises 1 partitions and 442 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 442
Gaps: 22.81 %
Invariant sites: 0.68 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24530/4_raxmlng_ancestral/P24530.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24530/3_mltree/P24530.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 111 / 8880
[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: -110382.484847

[00:00:00 -110382.484847] Initial branch length optimization
[00:00:00 -110161.334510] Model parameter optimization (eps = 0.100000)

[00:00:28] Tree #1, final logLikelihood: -109699.459839


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.239397,0.306526) (0.218064,0.448763) (0.300554,0.737104) (0.241985,2.509331) 
   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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24530/4_raxmlng_ancestral/P24530.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24530/4_raxmlng_ancestral/P24530.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24530/4_raxmlng_ancestral/P24530.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24530/4_raxmlng_ancestral/P24530.raxml.log

Analysis started: 02-Jun-2021 15:20:26 / finished: 02-Jun-2021 15:20:57

Elapsed time: 31.538 seconds