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 17:13:43 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/2_msa/P53804_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/3_mltree/P53804.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/4_raxmlng_ancestral/P53804 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626099223
  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/P53804/2_msa/P53804_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 2025 sites

WARNING: Sequences tr_B4Q623_B4Q623_DROSI_7240 and tr_B4ICV3_B4ICV3_DROSE_7238 are exactly identical!
WARNING: Sequences tr_M3Y1N6_M3Y1N6_MUSPF_9669 and tr_D2HL56_D2HL56_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3Y1N6_M3Y1N6_MUSPF_9669 and tr_A0A2U3VZE3_A0A2U3VZE3_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Y1N6_M3Y1N6_MUSPF_9669 and tr_A0A2Y9LDR3_A0A2Y9LDR3_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YGR5_M3YGR5_MUSPF_9669 and tr_A0A2Y9JV48_A0A2Y9JV48_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_B6Q8X2_B6Q8X2_TALMQ_441960 and tr_A0A093XQK2_A0A093XQK2_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_H2NU16_H2NU16_PONAB_9601 and sp_Q99615_DNJC7_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3RQR2_A0A2I3RQR2_PANTR_9598 and tr_A0A2R9BPI8_A0A2R9BPI8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A158NIE7_A0A158NIE7_ATTCE_12957 and tr_A0A151HZC0_A0A151HZC0_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158P267_A0A158P267_ATTCE_12957 and tr_A0A195AW63_A0A195AW63_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F6XI05_F6XI05_MACMU_9544 and tr_G7PXY4_G7PXY4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6XI05_F6XI05_MACMU_9544 and tr_A0A0D9S291_A0A0D9S291_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7XW48_G7XW48_ASPKW_1033177 and tr_A0A146EZE8_A0A146EZE8_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_I1R871_I1R871_ORYGL_4538 and tr_A0A0E0RKG7_A0A0E0RKG7_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1R871_I1R871_ORYGL_4538 and tr_A0A0D3HX53_A0A0D3HX53_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1R871_I1R871_ORYGL_4538 and tr_Q2QLM7_Q2QLM7_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G2Y1R0_G2Y1R0_BOTF4_999810 and tr_M7UTM8_M7UTM8_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_W2Q9H4_W2Q9H4_PHYPN_761204 and tr_A0A0W8D0C7_A0A0W8D0C7_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A015JP87_A0A015JP87_9GLOM_1432141 and tr_A0A2H5TVJ2_A0A2H5TVJ2_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2I3MUS9_A0A2I3MUS9_PAPAN_9555 and tr_A0A2K6AII1_A0A2K6AII1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A091E5Y9_A0A091E5Y9_CORBR_85066 and tr_A0A093SE08_A0A093SE08_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A091W7Q3_A0A091W7Q3_OPIHO_30419 and tr_A0A0A0A0N7_A0A0A0A0N7_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091W7Q3_A0A091W7Q3_OPIHO_30419 and tr_A0A091HNQ6_A0A091HNQ6_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A0V0VIR7_A0A0V0VIR7_9BILA_181606 and tr_A0A0V0TL13_A0A0V0TL13_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A100ISQ6_A0A100ISQ6_ASPNG_5061 and tr_A0A1L9NHC8_A0A1L9NHC8_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1S4BU78_A0A1S4BU78_TOBAC_4097 and tr_A0A1U7WHW4_A0A1U7WHW4_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2K6C0K4_A0A2K6C0K4_MACNE_9545 and tr_A0A2K5XFV7_A0A2K5XFV7_MANLE_9568 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/300621_run/phylogeny-snakemake/results/P53804/4_raxmlng_ancestral/P53804.raxml.reduced.phy

Alignment comprises 1 partitions and 2025 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 2025
Gaps: 73.76 %
Invariant sites: 0.05 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/4_raxmlng_ancestral/P53804.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/P53804/3_mltree/P53804.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 507 / 40560
[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: -392550.485713

[00:00:00 -392550.485713] Initial branch length optimization
[00:00:03 -389100.294475] Model parameter optimization (eps = 0.100000)

[00:02:59] Tree #1, final logLikelihood: -387200.618406


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.099009,0.610474) (0.054057,0.649227) (0.350264,0.692894) (0.496670,1.332407) 
   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/P53804/4_raxmlng_ancestral/P53804.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/4_raxmlng_ancestral/P53804.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/4_raxmlng_ancestral/P53804.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/4_raxmlng_ancestral/P53804.raxml.log

Analysis started: 12-Jul-2021 17:13:43 / finished: 12-Jul-2021 17:17:01

Elapsed time: 198.034 seconds

Consumed energy: 15.142 Wh