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 18-Jun-2021 00:10:54 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HCC0/2_msa/Q9HCC0_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HCC0/3_mltree/Q9HCC0.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HCC0/4_raxmlng_ancestral/Q9HCC0 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1623964254
  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/020621_run/phylogeny-snakemake/results/Q9HCC0/2_msa/Q9HCC0_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 563 sites

WARNING: Sequences tr_B4QDC4_B4QDC4_DROSI_7240 and tr_B4HQB5_B4HQB5_DROSE_7238 are exactly identical!
WARNING: Sequences tr_J3K8S0_J3K8S0_COCIM_246410 and tr_A0A0J6YAQ0_A0A0J6YAQ0_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QDP0_B6QDP0_TALMQ_441960 and tr_A0A093XN97_A0A093XN97_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2VUZ5_B2VUZ5_PYRTR_426418 and tr_A0A2W1EQM7_A0A2W1EQM7_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_A0A179U9N0_A0A179U9N0_BLAGS_559298 and tr_C5GJQ7_C5GJQ7_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2QR16_H2QR16_PANTR_9598 and tr_A0A2R9CTB8_A0A2R9CTB8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_C6HEU0_C6HEU0_AJECH_544712 and tr_F0ULU6_F0ULU6_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_Q2U451_Q2U451_ASPOR_510516 and tr_A0A1S9DHE3_A0A1S9DHE3_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A2QN36_A2QN36_ASPNC_425011 and tr_G3XYK9_G3XYK9_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QN36_A2QN36_ASPNC_425011 and tr_A0A319AR02_A0A319AR02_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XH31_G7XH31_ASPKW_1033177 and tr_A0A146F1Z5_A0A146F1Z5_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G2XNR2_G2XNR2_BOTF4_999810 and tr_M7UFV2_M7UFV2_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SMY2_F2SMY2_TRIRC_559305 and tr_D4AXH0_D4AXH0_ARTBC_663331 are exactly identical!
WARNING: Sequences tr_F2SMY2_F2SMY2_TRIRC_559305 and tr_A0A178F317_A0A178F317_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_N4TGS2_N4TGS2_FUSC1_1229664 and tr_X0CX02_X0CX02_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_N4TGS2_N4TGS2_FUSC1_1229664 and tr_A0A2H3TGR9_A0A2H3TGR9_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_N4TGS2_N4TGS2_FUSC1_1229664 and tr_A0A2H3GZA4_A0A2H3GZA4_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_U5HEA4_U5HEA4_USTV1_683840 and tr_A0A2X0LSR9_A0A2X0LSR9_9BASI_796604 are exactly identical!
WARNING: Sequences tr_W2QKS8_W2QKS8_PHYPN_761204 and tr_A0A0W8DB41_A0A0W8DB41_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QKS8_W2QKS8_PHYPN_761204 and tr_W2LT22_W2LT22_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015KLL7_A0A015KLL7_9GLOM_1432141 and tr_U9UXX4_U9UXX4_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A067EX65_A0A067EX65_CITSI_2711 and tr_V4SGW7_V4SGW7_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A084QS12_A0A084QS12_STAC4_1283841 and tr_A0A084RC61_A0A084RC61_STACH_1283842 are exactly identical!
WARNING: Sequences tr_A0A094H9N7_A0A094H9N7_9PEZI_1420912 and tr_A0A2P2SYF0_A0A2P2SYF0_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A1S3Z2C6_A0A1S3Z2C6_TOBAC_4097 and tr_A0A1U7W645_A0A1U7W645_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1U8DZI7_A0A1U8DZI7_CAPAN_4072 and tr_A0A2G3BV85_A0A2G3BV85_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2H5PRA8_A0A2H5PRA8_CITUN_55188 and tr_A0A2H5PRB3_A0A2H5PRB3_CITUN_55188 are exactly identical!
WARNING: Duplicate sequences found: 27

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HCC0/4_raxmlng_ancestral/Q9HCC0.raxml.reduced.phy

Alignment comprises 1 partitions and 563 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 563
Gaps: 8.09 %
Invariant sites: 0.18 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HCC0/4_raxmlng_ancestral/Q9HCC0.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/020621_run/phylogeny-snakemake/results/Q9HCC0/3_mltree/Q9HCC0.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 141 / 11280
[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: -221523.247243

[00:00:00 -221523.247243] Initial branch length optimization
[00:00:02 -217643.940946] Model parameter optimization (eps = 0.100000)

[00:00:36] Tree #1, final logLikelihood: -216602.183085


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.265139,0.317924) (0.335622,0.410086) (0.218797,1.155149) (0.180442,2.911347) 
   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/020621_run/phylogeny-snakemake/results/Q9HCC0/4_raxmlng_ancestral/Q9HCC0.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HCC0/4_raxmlng_ancestral/Q9HCC0.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HCC0/4_raxmlng_ancestral/Q9HCC0.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9HCC0/4_raxmlng_ancestral/Q9HCC0.raxml.log

Analysis started: 18-Jun-2021 00:10:54 / finished: 18-Jun-2021 00:11:36

Elapsed time: 42.148 seconds

Consumed energy: 3.562 Wh