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 03-Jun-2021 14:56:02 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96RG2/2_msa/Q96RG2_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96RG2/3_mltree/Q96RG2.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96RG2/4_raxmlng_ancestral/Q96RG2 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622721362
  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/Q96RG2/2_msa/Q96RG2_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1323 sites

WARNING: Sequences tr_A0A2I3H817_A0A2I3H817_NOMLE_61853 and tr_F7H0S2_F7H0S2_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3H817_A0A2I3H817_NOMLE_61853 and tr_A0A096N6L7_A0A096N6L7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3H817_A0A2I3H817_NOMLE_61853 and tr_A0A2K5NA70_A0A2K5NA70_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3H817_A0A2I3H817_NOMLE_61853 and tr_A0A2K6CTG1_A0A2K6CTG1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_J3KCF8_J3KCF8_COCIM_246410 and tr_A0A0J6YM31_A0A0J6YM31_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B8PJZ0_B8PJZ0_POSPM_561896 and tr_A0A1X6NCU1_A0A1X6NCU1_9APHY_670580 are exactly identical!
WARNING: Sequences tr_A0A0R3NFW7_A0A0R3NFW7_DROPS_46245 and tr_B4G6B1_B4G6B1_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A2I3RZW8_A0A2I3RZW8_PANTR_9598 and tr_A0A2K5LMN7_A0A2K5LMN7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2Q6S1_H2Q6S1_PANTR_9598 and sp_O60285_NUAK1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q6S1_H2Q6S1_PANTR_9598 and tr_A0A2R9AET3_A0A2R9AET3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_E9F0P1_E9F0P1_METRA_655844 and tr_A0A0D9NUE2_A0A0D9NUE2_METAN_1291518 are exactly identical!
WARNING: Sequences tr_A0A158NE68_A0A158NE68_ATTCE_12957 and tr_F4WM68_F4WM68_ACREC_103372 are exactly identical!
WARNING: Sequences tr_A0A158NE68_A0A158NE68_ATTCE_12957 and tr_A0A195BC10_A0A195BC10_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F4NYK6_F4NYK6_BATDJ_684364 and tr_A0A177WJ70_A0A177WJ70_BATDE_403673 are exactly identical!
WARNING: Sequences tr_G0PCD7_G0PCD7_CAEBE_135651 and tr_G0PD21_G0PD21_CAEBE_135651 are exactly identical!
WARNING: Sequences tr_A8WR86_A8WR86_CAEBR_6238 and tr_A0A2G5U7S6_A0A2G5U7S6_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_A0A3Q0KCJ0_A0A3Q0KCJ0_SCHMA_6183 and tr_G4LVH5_G4LVH5_SCHMA_6183 are exactly identical!
WARNING: Sequences tr_X0D213_X0D213_FUSOX_1089458 and tr_A0A2H3HIZ4_A0A2H3HIZ4_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A0F0HXN4_A0A0F0HXN4_ASPPU_1403190 and tr_A0A2G7FLK9_A0A2G7FLK9_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A0A1MQ03_A0A0A1MQ03_9FUNG_58291 and tr_A0A367KFR8_A0A367KFR8_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0A1N488_A0A0A1N488_9FUNG_58291 and tr_A0A367KCA6_A0A367KCA6_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0A1NF97_A0A0A1NF97_9FUNG_58291 and tr_A0A367K0J8_A0A367K0J8_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0V0SNW3_A0A0V0SNW3_9BILA_6336 and tr_A0A0V1DEN3_A0A0V1DEN3_TRIBR_45882 are exactly identical!
WARNING: Sequences tr_A0A0V0SNW3_A0A0V0SNW3_9BILA_6336 and tr_A0A0V0X6W5_A0A0V0X6W5_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V0SNW3_A0A0V0SNW3_9BILA_6336 and tr_A0A0V1LTQ6_A0A0V1LTQ6_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0SNW3_A0A0V0SNW3_9BILA_6336 and tr_A0A0V1PFS3_A0A0V1PFS3_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0VTX9_A0A0V0VTX9_9BILA_181606 and tr_A0A0V0UGN5_A0A0V0UGN5_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A100ID73_A0A100ID73_ASPNG_5061 and tr_A0A1L9MYT6_A0A1L9MYT6_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1S3NQZ4_A0A1S3NQZ4_SALSA_8030 and tr_A0A1S3SYE2_A0A1S3SYE2_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A226NPD3_A0A226NPD3_CALSU_9009 and tr_A0A226PTZ3_A0A226PTZ3_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0SYN1_A0A2D0SYN1_ICTPU_7998 and tr_A0A2D0SZ17_A0A2D0SZ17_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SYN1_A0A2D0SYN1_ICTPU_7998 and tr_A0A2D0SZK8_A0A2D0SZK8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U3VH39_A0A2U3VH39_ODORO_9708 and tr_A0A2Y9JNP1_A0A2Y9JNP1_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2Y9E0D5_A0A2Y9E0D5_TRIMA_127582 and tr_A0A2Y9EH17_A0A2Y9EH17_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 34

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/Q96RG2/4_raxmlng_ancestral/Q96RG2.raxml.reduced.phy

Alignment comprises 1 partitions and 1323 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 1323
Gaps: 58.02 %
Invariant sites: 0.30 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96RG2/4_raxmlng_ancestral/Q96RG2.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/Q96RG2/3_mltree/Q96RG2.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 331 / 26480
[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: -384310.702607

[00:00:00 -384310.702607] Initial branch length optimization
[00:00:03 -364682.246010] Model parameter optimization (eps = 0.100000)

[00:01:25] Tree #1, final logLikelihood: -363535.588308


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.094669,0.263373) (0.115695,0.302324) (0.263391,0.658745) (0.526244,1.456703) 
   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/Q96RG2/4_raxmlng_ancestral/Q96RG2.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96RG2/4_raxmlng_ancestral/Q96RG2.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96RG2/4_raxmlng_ancestral/Q96RG2.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96RG2/4_raxmlng_ancestral/Q96RG2.raxml.log

Analysis started: 03-Jun-2021 14:56:02 / finished: 03-Jun-2021 14:57:40

Elapsed time: 97.548 seconds

Consumed energy: 7.726 Wh