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 03-Jun-2021 02:43:46 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19878/2_msa/P19878_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19878/3_mltree/P19878.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19878/4_raxmlng_ancestral/P19878 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622677426
  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/P19878/2_msa/P19878_nogap_msa.fasta
[00:00:00] Loaded alignment with 1000 taxa and 526 sites

WARNING: Sequences sp_P97369_NCF4_MOUSE_10090 and tr_B2RZ98_B2RZ98_RAT_10116 are exactly identical!
WARNING: Sequences tr_J3K4A9_J3K4A9_COCIM_246410 and tr_A0A0J6YBW5_A0A0J6YBW5_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B2W9G1_B2W9G1_PYRTR_426418 and tr_A0A317BB07_A0A317BB07_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_Q7SBV8_Q7SBV8_NEUCR_367110 and tr_G4UNV2_G4UNV2_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_A0A2I3SYZ2_A0A2I3SYZ2_PANTR_9598 and tr_A0A2R9ALR4_A0A2R9ALR4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q0R6_H2Q0R6_PANTR_9598 and tr_A0A2R9BNV5_A0A2R9BNV5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9F3C0_F9F3C0_FUSOF_660025 and tr_A0A0D2Y5F9_A0A0D2Y5F9_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9F3C0_F9F3C0_FUSOF_660025 and tr_X0CG72_X0CG72_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9F3C0_F9F3C0_FUSOF_660025 and tr_A0A2H3TY28_A0A2H3TY28_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_C6HCV2_C6HCV2_AJECH_544712 and tr_F0UTL9_F0UTL9_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_J5JSS2_J5JSS2_BEAB2_655819 and tr_A0A0A2VJX6_A0A0A2VJX6_BEABA_1245745 are exactly identical!
WARNING: Sequences sp_A1DFN5_HSE1_NEOFI_331117 and tr_A0A0S7DT49_A0A0S7DT49_9EURO_293939 are exactly identical!
WARNING: Sequences sp_A2QW93_HSE1_ASPNC_425011 and tr_A0A319AAQ6_A0A319AAQ6_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A0A1D5Q5M3_A0A1D5Q5M3_MACMU_9544 and tr_A0A2K6BVL4_A0A2K6BVL4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5Q5M3_A0A1D5Q5M3_MACMU_9544 and tr_A0A2K6A330_A0A2K6A330_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6WJW0_F6WJW0_MACMU_9544 and tr_A0A2K6D9H6_A0A2K6D9H6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6WJW0_F6WJW0_MACMU_9544 and tr_A0A2K6ACU6_A0A2K6ACU6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7XAD1_G7XAD1_ASPKW_1033177 and tr_A0A100IJE0_A0A100IJE0_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XAD1_G7XAD1_ASPKW_1033177 and tr_A0A317W939_A0A317W939_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_G7XD13_G7XD13_ASPKW_1033177 and tr_A0A146FFP0_A0A146FFP0_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F4NRC5_F4NRC5_BATDJ_684364 and tr_A0A177W6U0_A0A177W6U0_BATDE_403673 are exactly identical!
WARNING: Sequences tr_G2YI10_G2YI10_BOTF4_999810 and tr_M7TVR7_M7TVR7_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2PPH4_F2PPH4_TRIEC_559882 and tr_A0A059J9Y1_A0A059J9Y1_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_S0EJU0_S0EJU0_GIBF5_1279085 and tr_A0A2K0WML4_A0A2K0WML4_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_S0EJU0_S0EJU0_GIBF5_1279085 and tr_A0A365NHQ0_A0A365NHQ0_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_N4TR96_N4TR96_FUSC1_1229664 and tr_A0A2H3H8J1_A0A2H3H8J1_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_U5H121_U5H121_USTV1_683840 and tr_A0A2X0MCP6_A0A2X0MCP6_9BASI_796604 are exactly identical!
WARNING: Sequences tr_V2XIZ8_V2XIZ8_MONRO_1381753 and tr_A0A0W0EXK2_A0A0W0EXK2_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A094E2D9_A0A094E2D9_9PEZI_1420912 and tr_A0A2P2SWA7_A0A2P2SWA7_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_I1RJU1_I1RJU1_GIBZE_229533 and tr_A0A2T4GUZ0_A0A2T4GUZ0_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A1S3NII3_A0A1S3NII3_SALSA_8030 and tr_C0H9S3_C0H9S3_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1V8V4L5_A0A1V8V4L5_9PEZI_1974281 and tr_A0A1V8S9P2_A0A1V8S9P2_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A319E1I0_A0A319E1I0_9EURO_1448315 and tr_A0A2V5II57_A0A2V5II57_9EURO_1450541 are exactly identical!
WARNING: Sequences tr_A0A319E1I0_A0A319E1I0_9EURO_1448315 and tr_A0A2V5H395_A0A2V5H395_9EURO_1450538 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/P19878/4_raxmlng_ancestral/P19878.raxml.reduced.phy

Alignment comprises 1 partitions and 526 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 526
Gaps: 40.60 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19878/4_raxmlng_ancestral/P19878.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/P19878/3_mltree/P19878.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 132 / 10560
[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: -262692.475658

[00:00:00 -262692.475658] Initial branch length optimization
[00:00:02 -208944.624268] Model parameter optimization (eps = 0.100000)

[00:00:52] Tree #1, final logLikelihood: -207637.545292


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.142717,0.446315) (0.103444,0.539530) (0.322068,0.597177) (0.431771,1.593809) 
   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/P19878/4_raxmlng_ancestral/P19878.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19878/4_raxmlng_ancestral/P19878.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19878/4_raxmlng_ancestral/P19878.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19878/4_raxmlng_ancestral/P19878.raxml.log

Analysis started: 03-Jun-2021 02:43:46 / finished: 03-Jun-2021 02:44:43

Elapsed time: 57.092 seconds

Consumed energy: 3.955 Wh