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 02-Jun-2021 18:18:55 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q05329/2_msa/Q05329_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q05329/3_mltree/Q05329.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q05329/4_raxmlng_ancestral/Q05329 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622647135
  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/Q05329/2_msa/Q05329_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 585 sites

WARNING: Sequences tr_M3XP05_M3XP05_MUSPF_9669 and tr_A0A2Y9JNZ7_A0A2Y9JNZ7_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YL68_M3YL68_MUSPF_9669 and tr_A0A2Y9IGD6_A0A2Y9IGD6_ENHLU_391180 are exactly identical!
WARNING: Sequences sp_P20228_DCE_DROME_7227 and tr_B4HTZ3_B4HTZ3_DROSE_7238 are exactly identical!
WARNING: Sequences tr_J3KC49_J3KC49_COCIM_246410 and tr_A0A0J6YLN9_A0A0J6YLN9_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B2W8X7_B2W8X7_PYRTR_426418 and tr_A0A2W1EKJ2_A0A2W1EKJ2_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_A0A2I2ZG24_A0A2I2ZG24_GORGO_9595 and sp_Q99259_DCE1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_C0NW51_C0NW51_AJECG_447093 and tr_C6HC58_C6HC58_AJECH_544712 are exactly identical!
WARNING: Sequences tr_C0NW51_C0NW51_AJECG_447093 and tr_F0UAU0_F0UAU0_AJEC8_544711 are exactly identical!
WARNING: Sequences sp_A0PA85_DCE1_CANLF_9615 and sp_P14748_DCE1_FELCA_9685 are exactly identical!
WARNING: Sequences tr_A0A2I3T2A5_A0A2I3T2A5_PANTR_9598 and tr_A0A2R9CDU3_A0A2R9CDU3_PANPA_9597 are exactly identical!
WARNING: Sequences sp_Q5IS68_DCE1_PANTR_9598 and tr_A0A2R9B9E1_A0A2R9B9E1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_J4KR63_J4KR63_BEAB2_655819 and tr_A0A0A2WF97_A0A0A2WF97_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_Q2UKU9_Q2UKU9_ASPOR_510516 and tr_A0A1S9DMI7_A0A1S9DMI7_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A0K0JMZ6_A0A0K0JMZ6_BRUMA_6279 and tr_A0A0N4TSZ2_A0A0N4TSZ2_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_A5AA79_A5AA79_ASPNC_425011 and tr_G3Y3H5_G3Y3H5_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A5AA79_A5AA79_ASPNC_425011 and tr_A0A319ARX0_A0A319ARX0_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A0A1D5QBA0_A0A1D5QBA0_MACMU_9544 and tr_A0A2K5NXE0_A0A2K5NXE0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QBA0_A0A1D5QBA0_MACMU_9544 and tr_A0A2K6CRX4_A0A2K6CRX4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6Q185_F6Q185_MACMU_9544 and tr_G7NYB1_G7NYB1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6Q185_F6Q185_MACMU_9544 and tr_A0A2K5YIZ7_A0A2K5YIZ7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7N8A4_G7N8A4_MACMU_9544 and tr_A0A2K5L252_A0A2K5L252_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7N8A4_G7N8A4_MACMU_9544 and tr_A0A2K6BBM7_A0A2K6BBM7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7N8A4_G7N8A4_MACMU_9544 and tr_A0A2K5ZTU7_A0A2K5ZTU7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7XPH0_G7XPH0_ASPKW_1033177 and tr_A0A146FC28_A0A146FC28_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F2SEL0_F2SEL0_TRIRC_559305 and tr_A0A178EU67_A0A178EU67_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_N4U434_N4U434_FUSC1_1229664 and tr_X0D1S8_X0D1S8_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0F8WP14_A0A0F8WP14_9EURO_308745 and tr_A0A2T5LZQ7_A0A2T5LZQ7_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A091J993_A0A091J993_EGRGA_188379 and tr_A0A091UXB1_A0A091UXB1_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A0V1D952_A0A0V1D952_TRIBR_45882 and tr_A0A0V1LBW5_A0A0V1LBW5_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1D952_A0A0V1D952_TRIBR_45882 and tr_A0A0V1A2A6_A0A0V1A2A6_9BILA_990121 are exactly identical!
WARNING: Duplicate sequences found: 30

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/Q05329/4_raxmlng_ancestral/Q05329.raxml.reduced.phy

Alignment comprises 1 partitions and 585 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 585
Gaps: 16.91 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q05329/4_raxmlng_ancestral/Q05329.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/Q05329/3_mltree/Q05329.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 147 / 11760
[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: -241167.270224

[00:00:00 -241167.270224] Initial branch length optimization
[00:00:01 -238773.187838] Model parameter optimization (eps = 0.100000)

[00:00:28] Tree #1, final logLikelihood: -238198.303246


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.151089,0.248226) (0.275566,0.360214) (0.238714,0.815496) (0.334632,1.997907) 
   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/Q05329/4_raxmlng_ancestral/Q05329.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q05329/4_raxmlng_ancestral/Q05329.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q05329/4_raxmlng_ancestral/Q05329.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q05329/4_raxmlng_ancestral/Q05329.raxml.log

Analysis started: 02-Jun-2021 18:18:55 / finished: 02-Jun-2021 18:19:29

Elapsed time: 33.671 seconds

Consumed energy: 2.658 Wh