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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 02-Jun-2021 18:14:36 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H2X9/2_msa/Q9H2X9_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H2X9/3_mltree/Q9H2X9.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H2X9/4_raxmlng_ancestral/Q9H2X9 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622646876
  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/Q9H2X9/2_msa/Q9H2X9_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1139 sites

WARNING: Sequences tr_M3Y9D9_M3Y9D9_MUSPF_9669 and tr_A0A2U3XGU3_A0A2U3XGU3_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3Y9D9_M3Y9D9_MUSPF_9669 and tr_A0A2Y9KY32_A0A2Y9KY32_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_D8RVK6_D8RVK6_SELML_88036 and tr_D8S2A3_D8S2A3_SELML_88036 are exactly identical!
WARNING: Sequences tr_A0A2I2Z741_A0A2I2Z741_GORGO_9595 and sp_Q9UHW9_S12A6_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3SRL5_A0A2I3SRL5_PANTR_9598 and sp_Q9H2X9_S12A5_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3SRL5_A0A2I3SRL5_PANTR_9598 and tr_A0A2R9CFZ8_A0A2R9CFZ8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0E0IA76_A0A0E0IA76_ORYNI_4536 and tr_I1QHL3_I1QHL3_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0IA76_A0A0E0IA76_ORYNI_4536 and tr_A0A0E0QHB7_A0A0E0QHB7_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0IA76_A0A0E0IA76_ORYNI_4536 and tr_A0A0D3GYY0_A0A0D3GYY0_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0IA76_A0A0E0IA76_ORYNI_4536 and tr_A0A0E0LTV6_A0A0E0LTV6_ORYPU_4537 are exactly identical!
WARNING: Sequences tr_A0A0E0IA76_A0A0E0IA76_ORYNI_4536 and sp_Q6Z0E2_CCC1_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F7H2L4_F7H2L4_MACMU_9544 and tr_G7PAP2_G7PAP2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7H2L4_F7H2L4_MACMU_9544 and tr_A0A2K6BU07_A0A2K6BU07_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H9FYQ0_H9FYQ0_MACMU_9544 and tr_A0A2K6BHT7_A0A2K6BHT7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0E0EK91_A0A0E0EK91_9ORYZ_40149 and tr_A0A0E0ATY4_A0A0E0ATY4_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_G0P7W2_G0P7W2_CAEBE_135651 and tr_G0PGY4_G0PGY4_CAEBE_135651 are exactly identical!
WARNING: Sequences tr_A0A096NTA1_A0A096NTA1_PAPAN_9555 and tr_A0A2K5MS19_A0A2K5MS19_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NTA1_A0A096NTA1_PAPAN_9555 and tr_A0A2K6AAQ5_A0A2K6AAQ5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3MFC4_A0A2I3MFC4_PAPAN_9555 and tr_A0A2K5NW84_A0A2K5NW84_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3MFC4_A0A2I3MFC4_PAPAN_9555 and tr_A0A2K6A7U7_A0A2K6A7U7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0V1D9H1_A0A0V1D9H1_TRIBR_45882 and tr_A0A0V0V4E5_A0A0V0V4E5_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1D9H1_A0A0V1D9H1_TRIBR_45882 and tr_A0A0V0ZFR6_A0A0V0ZFR6_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V1D9H1_A0A0V1D9H1_TRIBR_45882 and tr_A0A0V1P412_A0A0V1P412_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1D9H1_A0A0V1D9H1_TRIBR_45882 and tr_A0A0V0U5C7_A0A0V0U5C7_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1DIS9_A0A0V1DIS9_TRIBR_45882 and tr_A0A0V0W0C3_A0A0V0W0C3_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1DIS9_A0A0V1DIS9_TRIBR_45882 and tr_A0A0V1PPB0_A0A0V1PPB0_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A1S3M6F8_A0A1S3M6F8_SALSA_8030 and tr_A9NJG3_A9NJG3_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1I7T036_A0A1I7T036_9PELO_1561998 and tr_A0A1I7T037_A0A1I7T037_9PELO_1561998 are exactly identical!
WARNING: Duplicate sequences found: 28

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/Q9H2X9/4_raxmlng_ancestral/Q9H2X9.raxml.reduced.phy

Alignment comprises 1 partitions and 1139 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 1139
Gaps: 21.42 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H2X9/4_raxmlng_ancestral/Q9H2X9.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/Q9H2X9/3_mltree/Q9H2X9.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 285 / 22800
[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: -308239.043854

[00:00:00 -308239.043854] Initial branch length optimization
[00:00:01 -307834.902067] Model parameter optimization (eps = 0.100000)

[00:00:51] Tree #1, final logLikelihood: -306444.193219


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.226603,0.372560) (0.215284,0.414585) (0.316048,0.887184) (0.242065,2.255305) 
   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/Q9H2X9/4_raxmlng_ancestral/Q9H2X9.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H2X9/4_raxmlng_ancestral/Q9H2X9.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H2X9/4_raxmlng_ancestral/Q9H2X9.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H2X9/4_raxmlng_ancestral/Q9H2X9.raxml.log

Analysis started: 02-Jun-2021 18:14:36 / finished: 02-Jun-2021 18:15:38

Elapsed time: 62.428 seconds

Consumed energy: 3.220 Wh