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 31-Jul-2021 20:29:14 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P46934/2_msa/P46934_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P46934/3_mltree/P46934.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P46934/4_raxmlng_ancestral/P46934 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1627752554
  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_300621/phylogeny-snakemake/results/P46934/2_msa/P46934_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1319 sites

WARNING: Sequences tr_E3RQV3_E3RQV3_PYRTT_861557 and tr_B2W179_B2W179_PYRTR_426418 are exactly identical!
WARNING: Sequences tr_E3RQV3_E3RQV3_PYRTT_861557 and tr_A0A2W1DRQ7_A0A2W1DRQ7_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_C0NMQ2_C0NMQ2_AJECG_447093 and tr_F0U541_F0U541_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A179UHY6_A0A179UHY6_BLAGS_559298 and tr_C5GFJ5_C5GFJ5_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_K7BGN1_K7BGN1_PANTR_9598 and sp_Q96J02_ITCH_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_E9EJF9_E9EJF9_METRA_655844 and tr_A0A0B4HP08_A0A0B4HP08_METMF_1276143 are exactly identical!
WARNING: Sequences tr_E9EJF9_E9EJF9_METRA_655844 and tr_A0A0D9NSU6_A0A0D9NSU6_METAN_1291518 are exactly identical!
WARNING: Sequences tr_J4USV8_J4USV8_BEAB2_655819 and tr_A0A2N6P080_A0A2N6P080_BEABA_176275 are exactly identical!
WARNING: Sequences sp_A2QQ28_RSP5_ASPNC_425011 and tr_G3YFP8_G3YFP8_ASPNA_380704 are exactly identical!
WARNING: Sequences sp_A2QQ28_RSP5_ASPNC_425011 and tr_A0A319A8D3_A0A319A8D3_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_G7PGK1_G7PGK1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A096NUS9_A0A096NUS9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A2K5KTB2_A0A2K5KTB2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A2K6BGS2_A0A2K6BGS2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A2K5Z4A3_A0A2K5Z4A3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F9XPD8_F9XPD8_ZYMTI_336722 and tr_A0A1X7S762_A0A1X7S762_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YHG2_G2YHG2_BOTF4_999810 and tr_M7UZ78_M7UZ78_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A0D2XML3_A0A0D2XML3_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_S0E188_S0E188_GIBF5_1279085 are exactly identical!
WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_N4U0R5_N4U0R5_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_X0C902_X0C902_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A2H3SP11_A0A2H3SP11_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A2H3HCZ8_A0A2H3HCZ8_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A365NL61_A0A365NL61_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_V2X9P0_V2X9P0_MONRO_1381753 and tr_A0A0W0G149_A0A0W0G149_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A015LXQ7_A0A015LXQ7_9GLOM_1432141 and tr_A0A2I1FVZ7_A0A2I1FVZ7_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A094EJM6_A0A094EJM6_9PEZI_1420912 and tr_A0A1B8GLH3_A0A1B8GLH3_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0D9QVY0_A0A0D9QVY0_CHLSB_60711 and tr_A0A2K6AID8_A0A2K6AID8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A087QVU0_A0A087QVU0_APTFO_9233 and tr_A0A0A0AW30_A0A0A0AW30_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0G4P0J5_A0A0G4P0J5_PENCA_1429867 and tr_A0A1V6NEE6_A0A1V6NEE6_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A0L0RZ82_A0A0L0RZ82_ALLMA_578462 and tr_A0A0L0S7E5_A0A0L0S7E5_ALLMA_578462 are exactly identical!
WARNING: Sequences tr_I1S0N8_I1S0N8_GIBZE_229533 and tr_A0A2T4GIH5_A0A2T4GIH5_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A1V8UBZ0_A0A1V8UBZ0_9PEZI_1974281 and tr_A0A1V8SVT2_A0A1V8SVT2_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A2H3C4G0_A0A2H3C4G0_9AGAR_1076256 and tr_A0A284QUR2_A0A284QUR2_9AGAR_47428 are exactly identical!
WARNING: Sequences tr_A0A2U3ZN66_A0A2U3ZN66_ODORO_9708 and tr_A0A2Y9ILU8_A0A2Y9ILU8_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2U3ZN66_A0A2U3ZN66_ODORO_9708 and tr_A0A384CNI5_A0A384CNI5_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A2Y9T0Z2_A0A2Y9T0Z2_PHYCD_9755 and tr_A0A384B201_A0A384B201_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 37

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P46934/4_raxmlng_ancestral/P46934.raxml.reduced.phy

Alignment comprises 1 partitions and 1319 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 1319
Gaps: 44.59 %
Invariant sites: 1.52 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P46934/4_raxmlng_ancestral/P46934.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_300621/phylogeny-snakemake/results/P46934/3_mltree/P46934.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 330 / 26400
[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: -239493.156605

[00:00:00 -239493.156605] Initial branch length optimization
[00:00:02 -237817.541689] Model parameter optimization (eps = 0.100000)

[00:01:30] Tree #1, final logLikelihood: -237232.870705


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.135471,0.149368) (0.181369,0.247614) (0.239250,0.575592) (0.443909,1.795738) 
   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_300621/phylogeny-snakemake/results/P46934/4_raxmlng_ancestral/P46934.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P46934/4_raxmlng_ancestral/P46934.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P46934/4_raxmlng_ancestral/P46934.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P46934/4_raxmlng_ancestral/P46934.raxml.log

Analysis started: 31-Jul-2021 20:29:14 / finished: 31-Jul-2021 20:30:56

Elapsed time: 101.809 seconds