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 14:50:21 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P26440/2_msa/P26440_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P26440/3_mltree/P26440.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P26440/4_raxmlng_ancestral/P26440 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622634621
  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/P26440/2_msa/P26440_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 426 sites

WARNING: Sequences tr_B6QDP1_B6QDP1_TALMQ_441960 and tr_A0A093V2D6_A0A093V2D6_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2VV59_B2VV59_PYRTR_426418 and tr_A0A2W1H5N4_A0A2W1H5N4_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G3QI49_G3QI49_GORGO_9595 and sp_Q5RAS0_ACADS_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QI49_G3QI49_GORGO_9595 and tr_H2Q719_H2Q719_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QI49_G3QI49_GORGO_9595 and tr_A0A0D9S4L4_A0A0D9S4L4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3QI49_G3QI49_GORGO_9595 and tr_A0A2R8ZI63_A0A2R8ZI63_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q294T1_Q294T1_DROPS_46245 and tr_B4GMN1_B4GMN1_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q29CZ7_Q29CZ7_DROPS_46245 and tr_B4H9H6_B4H9H6_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B8NUG5_B8NUG5_ASPFN_332952 and tr_A0A1S9DHY9_A0A1S9DHY9_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UAD6_A0A179UAD6_BLAGS_559298 and tr_C5GJQ6_C5GJQ6_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_K7BSR9_K7BSR9_PANTR_9598 and tr_A0A2R9A7H7_A0A2R9A7H7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9G2H0_F9G2H0_FUSOF_660025 and tr_N4TEK8_N4TEK8_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9G2H0_F9G2H0_FUSOF_660025 and tr_A0A2H3TUA2_A0A2H3TUA2_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9G2H0_F9G2H0_FUSOF_660025 and tr_A0A2H3H6S9_A0A2H3H6S9_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A2QN37_A2QN37_ASPNC_425011 and tr_G3XYL0_G3XYL0_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QN37_A2QN37_ASPNC_425011 and tr_A0A319AY17_A0A319AY17_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_I1PS34_I1PS34_ORYGL_4538 and sp_Q75IM9_IVD_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G2XNR1_G2XNR1_BOTF4_999810 and tr_M7UPE2_M7UPE2_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SMY1_F2SMY1_TRIRC_559305 and tr_A0A178F2U9_A0A178F2U9_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_F2PU47_F2PU47_TRIEC_559882 and tr_A0A059JAT6_A0A059JAT6_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_U5H7K1_U5H7K1_USTV1_683840 and tr_A0A2X0M0R4_A0A2X0M0R4_9BASI_796604 are exactly identical!
WARNING: Sequences tr_A0A096NTG2_A0A096NTG2_PAPAN_9555 and tr_A0A2K6AZU8_A0A2K6AZU8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A094EQF1_A0A094EQF1_9PEZI_1420912 and tr_A0A2P2SYB8_A0A2P2SYB8_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0F0ILJ7_A0A0F0ILJ7_ASPPU_1403190 and tr_A0A2G7G4U0_A0A2G7G4U0_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A0F9XFV5_A0A0F9XFV5_TRIHA_5544 and tr_A0A2T3ZY15_A0A2T3ZY15_TRIHA_983964 are exactly identical!
WARNING: Sequences tr_A0A0G4PGS1_A0A0G4PGS1_PENCA_1429867 and tr_A0A1V6NM93_A0A1V6NM93_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A117DYH5_A0A117DYH5_ASPNG_5061 and tr_A0A1L9MY34_A0A1L9MY34_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1S3TKI8_A0A1S3TKI8_VIGRR_3916 and tr_A0A3Q0EVM3_A0A3Q0EVM3_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1B8E1Z4_A0A1B8E1Z4_9PEZI_1524831 and tr_A0A1B8C4W8_A0A1B8C4W8_9PEZI_1622147 are exactly identical!
WARNING: Sequences tr_A0A2G2YHX5_A0A2G2YHX5_CAPAN_4072 and tr_A0A2G3BBJ4_A0A2G3BBJ4_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2K5MUY9_A0A2K5MUY9_CERAT_9531 and tr_A0A2K5ZGT9_A0A2K5ZGT9_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 31

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/P26440/4_raxmlng_ancestral/P26440.raxml.reduced.phy

Alignment comprises 1 partitions and 426 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 426
Gaps: 8.00 %
Invariant sites: 1.88 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P26440/4_raxmlng_ancestral/P26440.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/P26440/3_mltree/P26440.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 107 / 8560
[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: -161811.249291

[00:00:00 -161811.249291] Initial branch length optimization
[00:00:01 -160248.142450] Model parameter optimization (eps = 0.100000)

[00:00:27] Tree #1, final logLikelihood: -159801.687334


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.247548,0.290886) (0.333109,0.458795) (0.209566,0.997021) (0.209777,2.699163) 
   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/P26440/4_raxmlng_ancestral/P26440.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P26440/4_raxmlng_ancestral/P26440.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P26440/4_raxmlng_ancestral/P26440.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P26440/4_raxmlng_ancestral/P26440.raxml.log

Analysis started: 02-Jun-2021 14:50:21 / finished: 02-Jun-2021 14:50:53

Elapsed time: 31.434 seconds