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 15:07:00 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UKY4/2_msa/Q9UKY4_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UKY4/3_mltree/Q9UKY4.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UKY4/4_raxmlng_ancestral/Q9UKY4 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622635620
  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/Q9UKY4/2_msa/Q9UKY4_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 750 sites

WARNING: Sequences tr_A0A0E1RZ86_A0A0E1RZ86_COCIM_246410 and tr_A0A0J6YS89_A0A0J6YS89_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B2W2E9_B2W2E9_PYRTR_426418 and tr_A0A2W1FAI3_A0A2W1FAI3_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_B2WAJ6_B2WAJ6_PYRTR_426418 and tr_A0A2W1HQS0_A0A2W1HQS0_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_Q1K4Z4_Q1K4Z4_NEUCR_367110 and tr_G4USV9_G4USV9_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_B8N5D6_B8N5D6_ASPFN_332952 and tr_Q2UBF4_Q2UBF4_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NV10_B8NV10_ASPFN_332952 and tr_A0A1S9DIC0_A0A1S9DIC0_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179US37_A0A179US37_BLAGS_559298 and tr_C5GPP0_C5GPP0_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2Q8P3_H2Q8P3_PANTR_9598 and tr_A0A2R9AB99_A0A2R9AB99_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FSL1_F9FSL1_FUSOF_660025 and tr_N4UBG2_N4UBG2_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FSL1_F9FSL1_FUSOF_660025 and tr_X0CS81_X0CS81_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FSL1_F9FSL1_FUSOF_660025 and tr_A0A2H3I029_A0A2H3I029_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_C6HLV2_C6HLV2_AJECH_544712 and tr_F0UPW3_F0UPW3_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_C6HQL6_C6HQL6_AJECH_544712 and tr_F0UMM0_F0UMM0_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A2QPR4_A2QPR4_ASPNC_425011 and tr_G3XZV9_G3XZV9_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QPR4_A2QPR4_ASPNC_425011 and tr_A0A319AM86_A0A319AM86_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A5ABN8_A5ABN8_ASPNC_425011 and tr_A0A319BZ89_A0A319BZ89_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XES9_G7XES9_ASPKW_1033177 and tr_A0A146F1Z6_A0A146F1Z6_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XFD5_G7XFD5_ASPKW_1033177 and tr_A0A146FQR0_A0A146FQR0_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F9X4M1_F9X4M1_ZYMTI_336722 and tr_A0A1X7RL87_A0A1X7RL87_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2Y3E2_G2Y3E2_BOTF4_999810 and tr_M7TKY8_M7TKY8_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_G2YTK5_G2YTK5_BOTF4_999810 and tr_M7TJS3_M7TJS3_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2STZ8_F2STZ8_TRIRC_559305 and tr_A0A178F7B9_A0A178F7B9_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_L0PGE8_L0PGE8_PNEJ8_1209962 and tr_A0A0W4ZMF8_A0A0W4ZMF8_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_S0DK98_S0DK98_GIBF5_1279085 and tr_A0A365MS83_A0A365MS83_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_V2WLU2_V2WLU2_MONRO_1381753 and tr_A0A0W0GFC5_A0A0W0GFC5_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A015IZF0_A0A015IZF0_9GLOM_1432141 and tr_U9TZC8_U9TZC8_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015JYS1_A0A015JYS1_9GLOM_1432141 and tr_A0A2H5R6B4_A0A2H5R6B4_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A094E0R3_A0A094E0R3_9PEZI_1420912 and tr_A0A1B8GMV5_A0A1B8GMV5_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0F8U9Q9_A0A0F8U9Q9_9EURO_308745 and tr_A0A2T5M069_A0A2T5M069_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0F8XKR8_A0A0F8XKR8_9EURO_308745 and tr_A0A2T5LXC4_A0A2T5LXC4_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A100ICF8_A0A100ICF8_ASPNG_5061 and tr_A0A1L9N041_A0A1L9N041_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A165AJN2_A0A165AJN2_9HOMO_1314777 and tr_A0A166IRP0_A0A166IRP0_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A2S7PEZ5_A0A2S7PEZ5_9HELO_2070414 and tr_A0A2S7R2R3_A0A2S7R2R3_9HELO_2070412 are exactly identical!
WARNING: Duplicate sequences found: 33

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/Q9UKY4/4_raxmlng_ancestral/Q9UKY4.raxml.reduced.phy

Alignment comprises 1 partitions and 750 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 750
Gaps: 9.85 %
Invariant sites: 2.40 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UKY4/4_raxmlng_ancestral/Q9UKY4.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/Q9UKY4/3_mltree/Q9UKY4.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 188 / 15040
[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: -332607.143718

[00:00:00 -332607.143718] Initial branch length optimization
[00:00:02 -330757.121409] Model parameter optimization (eps = 0.100000)

[00:03:22] Tree #1, final logLikelihood: -330062.327228


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.230162,0.270473) (0.289694,0.479795) (0.317853,1.258820) (0.162291,2.456297) 
   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/Q9UKY4/4_raxmlng_ancestral/Q9UKY4.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UKY4/4_raxmlng_ancestral/Q9UKY4.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UKY4/4_raxmlng_ancestral/Q9UKY4.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UKY4/4_raxmlng_ancestral/Q9UKY4.raxml.log

Analysis started: 02-Jun-2021 15:07:00 / finished: 02-Jun-2021 15:10:29

Elapsed time: 208.761 seconds