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 25-Jun-2021 16:00:40 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q92562/2_msa/Q92562_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q92562/3_mltree/Q92562.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q92562/4_raxmlng_ancestral/Q92562 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1624626040
  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_040621/phylogeny-snakemake/results/Q92562/2_msa/Q92562_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 907 sites

WARNING: Sequences tr_B6Q2W0_B6Q2W0_TALMQ_441960 and tr_A0A093UZ95_A0A093UZ95_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WG36_B2WG36_PYRTR_426418 and tr_A0A2W1FVL6_A0A2W1FVL6_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_Q29L99_Q29L99_DROPS_46245 and tr_B4GQF3_B4GQF3_DROPE_7234 are exactly identical!
WARNING: Sequences tr_E9ERV8_E9ERV8_METRA_655844 and tr_A0A0B4IJH5_A0A0B4IJH5_METMF_1276143 are exactly identical!
WARNING: Sequences tr_J4UQV1_J4UQV1_BEAB2_655819 and tr_A0A2N6NXD9_A0A2N6NXD9_BEABA_176275 are exactly identical!
WARNING: Sequences tr_Q2UB02_Q2UB02_ASPOR_510516 and tr_A0A1S9DSP0_A0A1S9DSP0_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_G7XZL9_G7XZL9_ASPKW_1033177 and tr_A0A100IRC2_A0A100IRC2_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XZL9_G7XZL9_ASPKW_1033177 and tr_A0A146F536_A0A146F536_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XZL9_G7XZL9_ASPKW_1033177 and tr_A0A1L9NEJ8_A0A1L9NEJ8_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_G7XZL9_G7XZL9_ASPKW_1033177 and tr_A0A317V754_A0A317V754_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_B8B3N6_B8B3N6_ORYSI_39946 and tr_A0A0E0PUM6_A0A0E0PUM6_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_B8B3N6_B8B3N6_ORYSI_39946 and tr_A0A0E0A687_A0A0E0A687_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_B8B3N6_B8B3N6_ORYSI_39946 and tr_Q69YB0_Q69YB0_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F2SRV6_F2SRV6_TRIRC_559305 and tr_A0A178EZT6_A0A178EZT6_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_G7P3N7_G7P3N7_MACFA_9541 and tr_A0A0D9RSD2_A0A0D9RSD2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7P3N7_G7P3N7_MACFA_9541 and tr_A0A2K5L7N2_A0A2K5L7N2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7P3N7_G7P3N7_MACFA_9541 and tr_A0A2K6EBU4_A0A2K6EBU4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_M4DIP6_M4DIP6_BRARP_51351 and tr_A0A078HS93_A0A078HS93_BRANA_3708 are exactly identical!
WARNING: Sequences tr_V2X4I3_V2X4I3_MONRO_1381753 and tr_A0A0W0FVL4_A0A0W0FVL4_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A078FH88_A0A078FH88_BRANA_3708 and tr_A0A0D3D7A8_A0A0D3D7A8_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A094F8E1_A0A094F8E1_9PEZI_1420912 and tr_A0A1B8GBH6_A0A1B8GBH6_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0F8UHL8_A0A0F8UHL8_9EURO_308745 and tr_A0A2T5LLV2_A0A2T5LLV2_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A1S4CJ80_A0A1S4CJ80_TOBAC_4097 and tr_A0A1U7Y1R1_A0A1U7Y1R1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3U4T8_A0A1S3U4T8_VIGRR_3916 and tr_A0A3Q0F1A4_A0A3Q0F1A4_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A2N5UZB9_A0A2N5UZB9_9BASI_200324 and tr_A0A2N5V5Z9_A0A2N5V5Z9_9BASI_200324 are exactly identical!
WARNING: Duplicate sequences found: 25

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q92562/4_raxmlng_ancestral/Q92562.raxml.reduced.phy

Alignment comprises 1 partitions and 907 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 907
Gaps: 23.01 %
Invariant sites: 0.99 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q92562/4_raxmlng_ancestral/Q92562.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_040621/phylogeny-snakemake/results/Q92562/3_mltree/Q92562.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 227 / 18160
[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: -335092.859812

[00:00:00 -335092.859812] Initial branch length optimization
[00:00:02 -331831.140785] Model parameter optimization (eps = 0.100000)

[00:00:41] Tree #1, final logLikelihood: -331243.845767


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.180335,0.197907) (0.182843,0.325791) (0.282328,0.749491) (0.354495,1.955290) 
   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_040621/phylogeny-snakemake/results/Q92562/4_raxmlng_ancestral/Q92562.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q92562/4_raxmlng_ancestral/Q92562.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q92562/4_raxmlng_ancestral/Q92562.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q92562/4_raxmlng_ancestral/Q92562.raxml.log

Analysis started: 25-Jun-2021 16:00:40 / finished: 25-Jun-2021 16:01:30

Elapsed time: 49.729 seconds