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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 01-Aug-2021 00:41:23 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TEQ0/2_msa/Q8TEQ0_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TEQ0/3_mltree/Q8TEQ0.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TEQ0/4_raxmlng_ancestral/Q8TEQ0 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1627767683
  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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TEQ0/2_msa/Q8TEQ0_nogap_msa.fasta
[00:00:00] Loaded alignment with 776 taxa and 813 sites

WARNING: Sequences tr_B4QGE1_B4QGE1_DROSI_7240 and tr_B4HRU1_B4HRU1_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B6QQY3_B6QQY3_TALMQ_441960 and tr_A0A093XHN9_A0A093XHN9_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_G3SKQ3_G3SKQ3_GORGO_9595 and tr_H2PMZ7_H2PMZ7_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3SKQ3_G3SKQ3_GORGO_9595 and tr_A0A2I3S077_A0A2I3S077_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3SKQ3_G3SKQ3_GORGO_9595 and sp_Q96NL0_RUN3B_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3SKQ3_G3SKQ3_GORGO_9595 and tr_A0A096NZX7_A0A096NZX7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3SKQ3_G3SKQ3_GORGO_9595 and tr_A0A2K5LUH7_A0A2K5LUH7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3SKQ3_G3SKQ3_GORGO_9595 and tr_A0A2K6A262_A0A2K6A262_MANLE_9568 are exactly identical!
WARNING: Sequences tr_Q290Z5_Q290Z5_DROPS_46245 and tr_B4GB09_B4GB09_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A179ULN7_A0A179ULN7_BLAGS_559298 and tr_C5GAD1_C5GAD1_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F1PCA7_F1PCA7_CANLF_9615 and tr_D2GY19_D2GY19_AILME_9646 are exactly identical!
WARNING: Sequences tr_H2QD91_H2QD91_PANTR_9598 and tr_A0A2R9C6Q4_A0A2R9C6Q4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A158NWD5_A0A158NWD5_ATTCE_12957 and tr_A0A151I5A7_A0A151I5A7_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F6UUH3_F6UUH3_MACMU_9544 and tr_A0A2K6C681_A0A2K6C681_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7H3W4_F7H3W4_MACMU_9544 and tr_G7P1V7_G7P1V7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7H3W4_F7H3W4_MACMU_9544 and tr_A0A2K6AS71_A0A2K6AS71_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G9MIS9_G9MIS9_HYPVG_413071 and tr_A0A2T4AD27_A0A2T4AD27_TRIHA_983964 are exactly identical!
WARNING: Sequences tr_H0ZUH3_H0ZUH3_TAEGU_59729 and tr_A0A091ENP5_A0A091ENP5_CORBR_85066 are exactly identical!
WARNING: Sequences tr_A0A0D9QUN9_A0A0D9QUN9_CHLSB_60711 and tr_A0A2K5L510_A0A2K5L510_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0F8XM26_A0A0F8XM26_9EURO_308745 and tr_A0A2T5M1J2_A0A2T5M1J2_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A091J5X2_A0A091J5X2_EGRGA_188379 and tr_A0A0A0AWG2_A0A0A0AWG2_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091URB8_A0A091URB8_NIPNI_128390 and tr_A0A087QT95_A0A087QT95_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A093HDN8_A0A093HDN8_STRCA_441894 and tr_A0A099ZP66_A0A099ZP66_TINGU_94827 are exactly identical!
WARNING: Sequences tr_A0A1S3I2R1_A0A1S3I2R1_LINUN_7574 and tr_A0A1S3I3Z6_A0A1S3I3Z6_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A2D0PHW0_A0A2D0PHW0_ICTPU_7998 and tr_A0A2D0PJC5_A0A2D0PJC5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RAB2_A0A2D0RAB2_ICTPU_7998 and tr_A0A2D0RBI9_A0A2D0RBI9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U3WPH8_A0A2U3WPH8_ODORO_9708 and tr_A0A2Y9JEN3_A0A2Y9JEN3_ENHLU_391180 are exactly identical!
WARNING: Duplicate sequences found: 27

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TEQ0/4_raxmlng_ancestral/Q8TEQ0.raxml.reduced.phy

Alignment comprises 1 partitions and 813 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 813
Gaps: 44.03 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TEQ0/4_raxmlng_ancestral/Q8TEQ0.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TEQ0/3_mltree/Q8TEQ0.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 204 / 16320
[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: -246449.493149

[00:00:00 -246449.493149] Initial branch length optimization
[00:00:01 -244374.603024] Model parameter optimization (eps = 0.100000)

[00:00:57] Tree #1, final logLikelihood: -243690.324014


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.098361,0.830304) (0.059121,0.411065) (0.397352,0.654719) (0.445166,1.423904) 
   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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TEQ0/4_raxmlng_ancestral/Q8TEQ0.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TEQ0/4_raxmlng_ancestral/Q8TEQ0.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TEQ0/4_raxmlng_ancestral/Q8TEQ0.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TEQ0/4_raxmlng_ancestral/Q8TEQ0.raxml.log

Analysis started: 01-Aug-2021 00:41:23 / finished: 01-Aug-2021 00:42:26

Elapsed time: 62.913 seconds