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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 12-Jul-2021 17:48:10 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2Z4/2_msa/Q9Y2Z4_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2Z4/3_mltree/Q9Y2Z4.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2Z4/4_raxmlng_ancestral/Q9Y2Z4 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626101290
  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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2Z4/2_msa/Q9Y2Z4_nogap_msa.fasta
[00:00:00] Loaded alignment with 914 taxa and 477 sites

WARNING: Sequences tr_J3K6A2_J3K6A2_COCIM_246410 and tr_A0A0J6YIW9_A0A0J6YIW9_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B8N9I8_B8N9I8_ASPFN_332952 and tr_A0A1S9DZC8_A0A1S9DZC8_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_E9F5B4_E9F5B4_METRA_655844 and tr_A0A0B4I2I1_A0A0B4I2I1_METMF_1276143 are exactly identical!
WARNING: Sequences tr_E9F5B4_E9F5B4_METRA_655844 and tr_A0A0D9NP20_A0A0D9NP20_METAN_1291518 are exactly identical!
WARNING: Sequences tr_C6H230_C6H230_AJECH_544712 and tr_F0U4I3_F0U4I3_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A2QIC2_A2QIC2_ASPNC_425011 and tr_G3Y8W1_G3Y8W1_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QIC2_A2QIC2_ASPNC_425011 and tr_A0A319AH97_A0A319AH97_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_H9H3M7_H9H3M7_MACMU_9544 and tr_G7PHL0_G7PHL0_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7X7J6_G7X7J6_ASPKW_1033177 and tr_A0A146FHR0_A0A146FHR0_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7X7J6_G7X7J6_ASPKW_1033177 and tr_A0A317UY82_A0A317UY82_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A2WQF7_A2WQF7_ORYSI_39946 and tr_A0A0D9Y964_A0A0D9Y964_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A2WQF7_A2WQF7_ORYSI_39946 and tr_Q943W5_Q943W5_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G2Y941_G2Y941_BOTF4_999810 and tr_M7UNG0_M7UNG0_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_A0A0D2XB08_A0A0D2XB08_FUSO4_426428 and tr_N4TVE2_N4TVE2_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_A0A0D2XB08_A0A0D2XB08_FUSO4_426428 and tr_X0CZN3_X0CZN3_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0D2XB08_A0A0D2XB08_FUSO4_426428 and tr_A0A2H3SRJ1_A0A2H3SRJ1_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A0A0D2XB08_A0A0D2XB08_FUSO4_426428 and tr_A0A2H3I9L0_A0A2H3I9L0_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_S0DKF9_S0DKF9_GIBF5_1279085 and tr_A0A365MUZ2_A0A365MUZ2_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_A0A096NBK8_A0A096NBK8_PAPAN_9555 and tr_A0A2K5N519_A0A2K5N519_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A094END2_A0A094END2_9PEZI_1420912 and tr_A0A1B8GHA9_A0A1B8GHA9_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0D2R0M9_A0A0D2R0M9_GOSRA_29730 and tr_A0A1U8LNM5_A0A1U8LNM5_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0F8V361_A0A0F8V361_9EURO_308745 and tr_A0A2T5M6A6_A0A2T5M6A6_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0V0VPM8_A0A0V0VPM8_9BILA_181606 and tr_A0A0V0U9F0_A0A0V0U9F0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_I1RB39_I1RB39_GIBZE_229533 and tr_A0A2T4H988_A0A2T4H988_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A1S4B6Z5_A0A1S4B6Z5_TOBAC_4097 and tr_A0A1U7VEC2_A0A1U7VEC2_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2N5SYD2_A0A2N5SYD2_9BASI_200324 and tr_A0A2N5W2Z1_A0A2N5W2Z1_9BASI_200324 are exactly identical!
WARNING: Duplicate sequences found: 26

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2Z4/4_raxmlng_ancestral/Q9Y2Z4.raxml.reduced.phy

Alignment comprises 1 partitions and 477 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 477
Gaps: 15.57 %
Invariant sites: 0.84 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2Z4/4_raxmlng_ancestral/Q9Y2Z4.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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2Z4/3_mltree/Q9Y2Z4.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 120 / 9600
[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: -269044.962272

[00:00:00 -269044.962272] Initial branch length optimization
[00:00:01 -268100.228439] Model parameter optimization (eps = 0.100000)

[00:00:45] Tree #1, final logLikelihood: -267597.335859


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.156345,0.274822) (0.233291,0.414686) (0.269698,0.802038) (0.340666,1.890364) 
   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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2Z4/4_raxmlng_ancestral/Q9Y2Z4.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2Z4/4_raxmlng_ancestral/Q9Y2Z4.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2Z4/4_raxmlng_ancestral/Q9Y2Z4.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2Z4/4_raxmlng_ancestral/Q9Y2Z4.raxml.log

Analysis started: 12-Jul-2021 17:48:10 / finished: 12-Jul-2021 17:49:00

Elapsed time: 49.304 seconds

Consumed energy: 4.273 Wh