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 04-Jun-2021 14:13:56 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51687/2_msa/P51687_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51687/3_mltree/P51687.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51687/4_raxmlng_ancestral/P51687 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622805236
  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/P51687/2_msa/P51687_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 545 sites

WARNING: Sequences tr_B8P4B3_B8P4B3_POSPM_561896 and tr_A0A1X6MN04_A0A1X6MN04_9APHY_670580 are exactly identical!
WARNING: Sequences tr_A0A179UD61_A0A179UD61_BLAGS_559298 and tr_C5GIM2_C5GIM2_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2R2S8_H2R2S8_PANTR_9598 and tr_A0A2R8ZFM7_A0A2R8ZFM7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9F651_F9F651_FUSOF_660025 and tr_A0A2H3TQD0_A0A2H3TQD0_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_C6HFC5_C6HFC5_AJECH_544712 and tr_F0UP25_F0UP25_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A0E0GDD5_A0A0E0GDD5_ORYNI_4536 and tr_B8AJ60_B8AJ60_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0GDD5_A0A0E0GDD5_ORYNI_4536 and tr_I1P4P3_I1P4P3_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0GDD5_A0A0E0GDD5_ORYNI_4536 and tr_A0A0E0CS18_A0A0E0CS18_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0GDD5_A0A0E0GDD5_ORYNI_4536 and tr_A0A0E0NLH4_A0A0E0NLH4_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GDD5_A0A0E0GDD5_ORYNI_4536 and tr_A0A0D3FB03_A0A0D3FB03_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0IEZ3_A0A0E0IEZ3_ORYNI_4536 and tr_A0A0E0QLK9_A0A0E0QLK9_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0IEZ3_A0A0E0IEZ3_ORYNI_4536 and tr_Q8LP96_Q8LP96_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A5AB36_A5AB36_ASPNC_425011 and tr_A0A319AC37_A0A319AC37_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A0A2K1JYE3_A0A2K1JYE3_PHYPA_3218 and tr_Q4LEW9_Q4LEW9_PHYPA_3218 are exactly identical!
WARNING: Sequences tr_F9X6E2_F9X6E2_ZYMTI_336722 and tr_A0A1X7RP70_A0A1X7RP70_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_F2SN51_F2SN51_TRIRC_559305 and tr_A0A178F429_A0A178F429_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_B3RRA2_B3RRA2_TRIAD_10228 and tr_A0A369SFB2_A0A369SFB2_9METZ_287889 are exactly identical!
WARNING: Sequences tr_M4CVT6_M4CVT6_BRARP_51351 and tr_A0A0D3ARC1_A0A0D3ARC1_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_W2PIH1_W2PIH1_PHYPN_761204 and tr_W2FU31_W2FU31_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2PLE7_W2PLE7_PHYPN_761204 and tr_A0A0W8BXR4_A0A0W8BXR4_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PLE7_W2PLE7_PHYPN_761204 and tr_W2KAP8_W2KAP8_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015LM07_A0A015LM07_9GLOM_1432141 and tr_A0A2H5S1K3_A0A2H5S1K3_RHIID_747089 are exactly identical!
WARNING: Sequences tr_X0BC91_X0BC91_FUSOX_1089458 and tr_A0A2H3SYR2_A0A2H3SYR2_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A0A0V1DBY5_A0A0V1DBY5_TRIBR_45882 and tr_A0A0V0U0I5_A0A0V0U0I5_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S3ZD90_A0A1S3ZD90_TOBAC_4097 and sp_P08509_NIA2_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S3ZD90_A0A1S3ZD90_TOBAC_4097 and tr_A0A1U7UPF8_A0A1U7UPF8_NICSY_4096 are exactly identical!
WARNING: Duplicate sequences found: 26

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/P51687/4_raxmlng_ancestral/P51687.raxml.reduced.phy

Alignment comprises 1 partitions and 545 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 545
Gaps: 24.05 %
Invariant sites: 0.92 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51687/4_raxmlng_ancestral/P51687.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/P51687/3_mltree/P51687.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 137 / 10960
[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: -257399.739496

[00:00:00 -257399.739496] Initial branch length optimization
[00:00:01 -256820.719418] Model parameter optimization (eps = 0.100000)

[00:06:42] Tree #1, final logLikelihood: -256186.749147


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.160640,0.249028) (0.186802,0.373693) (0.283803,0.824136) (0.368754,1.779769) 
   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/P51687/4_raxmlng_ancestral/P51687.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51687/4_raxmlng_ancestral/P51687.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51687/4_raxmlng_ancestral/P51687.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P51687/4_raxmlng_ancestral/P51687.raxml.log

Analysis started: 04-Jun-2021 14:13:56 / finished: 04-Jun-2021 14:20:43

Elapsed time: 407.117 seconds