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 20-Jul-2021 16:32:46 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16795/2_msa/Q16795_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16795/3_mltree/Q16795.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16795/4_raxmlng_ancestral/Q16795 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626787966
  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/Q16795/2_msa/Q16795_nogap_msa.fasta
[00:00:00] Loaded alignment with 932 taxa and 377 sites

WARNING: Sequences tr_A0A0E1S573_A0A0E1S573_COCIM_246410 and tr_A0A0J6Y1Y2_A0A0J6Y1Y2_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QDM4_B6QDM4_TALMQ_441960 and tr_A0A093V3F4_A0A093V3F4_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_G2WVI7_G2WVI7_VERDV_498257 and tr_C9SRB3_C9SRB3_VERA1_526221 are exactly identical!
WARNING: Sequences tr_B8N225_B8N225_ASPFN_332952 and tr_A0A1S9DNC1_A0A1S9DNC1_ASPOZ_5062 are exactly identical!
WARNING: Sequences sp_Q0MQB4_NDUA9_PANTR_9598 and tr_A0A2R9BL14_A0A2R9BL14_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FCF5_F9FCF5_FUSOF_660025 and tr_A0A0D2XIF6_A0A0D2XIF6_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FCF5_F9FCF5_FUSOF_660025 and tr_X0D3X2_X0D3X2_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FCF5_F9FCF5_FUSOF_660025 and tr_A0A2H3HQM6_A0A2H3HQM6_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_F9FCF5_F9FCF5_FUSOF_660025 and tr_A0A365NK16_A0A365NK16_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_J4UEM1_J4UEM1_BEAB2_655819 and tr_A0A0A2V3J4_A0A0A2V3J4_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_A0A158N9J6_A0A158N9J6_ATTCE_12957 and tr_A0A151I416_A0A151I416_9HYME_520822 are exactly identical!
WARNING: Sequences tr_G7XLY9_G7XLY9_ASPKW_1033177 and tr_A0A100IQ03_A0A100IQ03_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XLY9_G7XLY9_ASPKW_1033177 and tr_A0A146F9B3_A0A146F9B3_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XLY9_G7XLY9_ASPKW_1033177 and tr_A0A1L9NQ82_A0A1L9NQ82_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_I1P5J5_I1P5J5_ORYGL_4538 and tr_A0A0E0NMU0_A0A0E0NMU0_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1P5J5_I1P5J5_ORYGL_4538 and tr_A0A0D3FC23_A0A0D3FC23_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1P5J5_I1P5J5_ORYGL_4538 and tr_Q6K6A4_Q6K6A4_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F9XMV6_F9XMV6_ZYMTI_336722 and tr_A0A0F4GR07_A0A0F4GR07_9PEZI_1047168 are exactly identical!
WARNING: Sequences tr_F9XMV6_F9XMV6_ZYMTI_336722 and tr_A0A1X7S6B0_A0A1X7S6B0_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G3YFU3_G3YFU3_ASPNA_380704 and tr_A0A319A0F8_A0A319A0F8_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_L2FFX9_L2FFX9_COLFN_1213859 and tr_T0KFM1_T0KFM1_COLGC_1237896 are exactly identical!
WARNING: Sequences tr_V2X6Z3_V2X6Z3_MONRO_1381753 and tr_A0A0W0EV77_A0A0W0EV77_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A094DBI2_A0A094DBI2_9PEZI_1420910 and tr_A0A1B8EME5_A0A1B8EME5_9PEZI_1622149 are exactly identical!
WARNING: Sequences tr_A0A0F9XCE6_A0A0F9XCE6_TRIHA_5544 and tr_A0A2T3ZX00_A0A2T3ZX00_TRIHA_983964 are exactly identical!
WARNING: Sequences tr_A0A0F8WWK6_A0A0F8WWK6_9EURO_308745 and tr_A0A2T5LPB9_A0A2T5LPB9_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0V1CA79_A0A0V1CA79_TRIBR_45882 and tr_A0A0V0U358_A0A0V0U358_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1V8TVV9_A0A1V8TVV9_9PEZI_1974281 and tr_A0A1V8TA05_A0A1V8TA05_9PEZI_1507870 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/Q16795/4_raxmlng_ancestral/Q16795.raxml.reduced.phy

Alignment comprises 1 partitions and 377 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 377
Gaps: 13.73 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16795/4_raxmlng_ancestral/Q16795.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/Q16795/3_mltree/Q16795.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 95 / 7600
[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: -172477.390729

[00:00:00 -172477.390729] Initial branch length optimization
[00:00:00 -172127.184826] Model parameter optimization (eps = 0.100000)

[00:00:27] Tree #1, final logLikelihood: -171312.143482


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.182159,0.427520) (0.198842,0.510556) (0.398971,1.018354) (0.220027,1.882991) 
   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/Q16795/4_raxmlng_ancestral/Q16795.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16795/4_raxmlng_ancestral/Q16795.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16795/4_raxmlng_ancestral/Q16795.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16795/4_raxmlng_ancestral/Q16795.raxml.log

Analysis started: 20-Jul-2021 16:32:46 / finished: 20-Jul-2021 16:33:16

Elapsed time: 30.505 seconds