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 14-Jul-2021 16:55:24 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NRW7/2_msa/Q9NRW7_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NRW7/3_mltree/Q9NRW7.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NRW7/4_raxmlng_ancestral/Q9NRW7 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626270924
  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/Q9NRW7/2_msa/Q9NRW7_nogap_msa.fasta
[00:00:00] Loaded alignment with 958 taxa and 570 sites

WARNING: Sequences tr_M3Y200_M3Y200_MUSPF_9669 and tr_A0A2Y9L6K3_A0A2Y9L6K3_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A0E1S5P8_A0A0E1S5P8_COCIM_246410 and tr_A0A0J7AXQ5_A0A0J7AXQ5_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QVA6_B6QVA6_TALMQ_441960 and tr_A0A093UQ37_A0A093UQ37_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2VVC5_B2VVC5_PYRTR_426418 and tr_A0A2W1GW64_A0A2W1GW64_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_H2N605_H2N605_PONAB_9601 and tr_A0A2I3TKP9_A0A2I3TKP9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2N605_H2N605_PONAB_9601 and tr_A0A2R9BVC6_A0A2R9BVC6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_B8ND41_B8ND41_ASPFN_332952 and tr_Q2U9F2_Q2U9F2_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8ND41_B8ND41_ASPFN_332952 and tr_A0A1S9DAC6_A0A1S9DAC6_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UZ08_A0A179UZ08_BLAGS_559298 and tr_C5GLP7_C5GLP7_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_G7XZ62_G7XZ62_ASPKW_1033177 and tr_A0A117DZJ8_A0A117DZJ8_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XZ62_G7XZ62_ASPKW_1033177 and tr_A0A146FZ49_A0A146FZ49_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XZ62_G7XZ62_ASPKW_1033177 and tr_A0A1L9UBY2_A0A1L9UBY2_9EURO_767769 are exactly identical!
WARNING: Sequences tr_G7XZ62_G7XZ62_ASPKW_1033177 and tr_A0A317VXU7_A0A317VXU7_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_B8AH63_B8AH63_ORYSI_39946 and tr_Q6ZGF2_Q6ZGF2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F9XHG8_F9XHG8_ZYMTI_336722 and tr_A0A1X7S0S8_A0A1X7S0S8_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YJ43_G2YJ43_BOTF4_999810 and tr_M7U977_M7U977_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_G3XXE9_G3XXE9_ASPNA_380704 and tr_A0A319BHU3_A0A319BHU3_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7NTS3_G7NTS3_MACFA_9541 and tr_A0A096N7B5_A0A096N7B5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7NTS3_G7NTS3_MACFA_9541 and tr_A0A0D9RZT7_A0A0D9RZT7_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7NTS3_G7NTS3_MACFA_9541 and tr_A0A2K6CLH3_A0A2K6CLH3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_M4CVP7_M4CVP7_BRARP_51351 and tr_A0A0D3AR52_A0A0D3AR52_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_W2QH80_W2QH80_PHYPN_761204 and tr_A0A0W8CKT3_A0A0W8CKT3_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A015LAK2_A0A015LAK2_9GLOM_1432141 and tr_U9TB99_U9TB99_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A094E8Y7_A0A094E8Y7_9PEZI_1420912 and tr_A0A1B8GI35_A0A1B8GI35_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_X0DCB6_X0DCB6_FUSOX_1089458 and tr_A0A2H3SL62_A0A2H3SL62_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A0A0D2VDD7_A0A0D2VDD7_GOSRA_29730 and tr_A0A1U8NSM0_A0A1U8NSM0_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0F8XEK5_A0A0F8XEK5_9EURO_308745 and tr_A0A2T5LR06_A0A2T5LR06_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A1S4AAU6_A0A1S4AAU6_TOBAC_4097 and tr_A0A1U7VQ39_A0A1U7VQ39_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1U8GE37_A0A1U8GE37_CAPAN_4072 and tr_A0A2G3CMU2_A0A2G3CMU2_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2K5M0T0_A0A2K5M0T0_CERAT_9531 and tr_A0A2K5XJ99_A0A2K5XJ99_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 30

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/Q9NRW7/4_raxmlng_ancestral/Q9NRW7.raxml.reduced.phy

Alignment comprises 1 partitions and 570 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 570
Gaps: 10.05 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NRW7/4_raxmlng_ancestral/Q9NRW7.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/Q9NRW7/3_mltree/Q9NRW7.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 143 / 11440
[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: -241069.503649

[00:00:00 -241069.503649] Initial branch length optimization
[00:00:00 -240693.736473] Model parameter optimization (eps = 0.100000)

[00:00:34] Tree #1, final logLikelihood: -239733.622759


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.210546,0.418627) (0.247545,0.605453) (0.304457,0.956861) (0.237452,1.982125) 
   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/Q9NRW7/4_raxmlng_ancestral/Q9NRW7.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NRW7/4_raxmlng_ancestral/Q9NRW7.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NRW7/4_raxmlng_ancestral/Q9NRW7.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NRW7/4_raxmlng_ancestral/Q9NRW7.raxml.log

Analysis started: 14-Jul-2021 16:55:24 / finished: 14-Jul-2021 16:56:03

Elapsed time: 39.269 seconds