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 02-Jun-2021 14:58:08 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UQ90/2_msa/Q9UQ90_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UQ90/3_mltree/Q9UQ90.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UQ90/4_raxmlng_ancestral/Q9UQ90 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622635088
  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_020621/phylogeny-snakemake/results/Q9UQ90/2_msa/Q9UQ90_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 795 sites

WARNING: Sequences tr_A0A0R3P5M1_A0A0R3P5M1_DROPS_46245 and tr_B4H641_B4H641_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2QEA1_H2QEA1_PANTR_9598 and sp_Q9Y4W6_AFG32_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QEA1_H2QEA1_PANTR_9598 and tr_A0A2R8Z921_A0A2R8Z921_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FTD6_F9FTD6_FUSOF_660025 and tr_N4U6Q0_N4U6Q0_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FTD6_F9FTD6_FUSOF_660025 and tr_A0A2H3T3X4_A0A2H3T3X4_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_J5JEI6_J5JEI6_BEAB2_655819 and tr_A0A0A2VM53_A0A0A2VM53_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_A0A158NAG8_A0A158NAG8_ATTCE_12957 and tr_A0A151I0W7_A0A151I0W7_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A0E0HFJ2_A0A0E0HFJ2_ORYNI_4536 and tr_A0A0E0A095_A0A0E0A095_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0HFJ2_A0A0E0HFJ2_ORYNI_4536 and sp_Q0DHL4_FTSH8_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0K0JN58_A0A0K0JN58_BRUMA_6279 and tr_A0A158PT21_A0A158PT21_9BILA_42155 are exactly identical!
WARNING: Sequences tr_F4NTN6_F4NTN6_BATDJ_684364 and tr_A0A177WD41_A0A177WD41_BATDE_403673 are exactly identical!
WARNING: Sequences tr_G2XWR1_G2XWR1_BOTF4_999810 and tr_M7THM5_M7THM5_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_A0A0D2XDM8_A0A0D2XDM8_FUSO4_426428 and tr_X0D253_X0D253_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_V2XYM3_V2XYM3_MONRO_1381753 and tr_A0A0W0FGP4_A0A0W0FGP4_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2Q8K1_W2Q8K1_PHYPN_761204 and tr_A0A0W8CIB5_A0A0W8CIB5_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2Q8K1_W2Q8K1_PHYPN_761204 and tr_W2NEC3_W2NEC3_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A0D2QC48_A0A0D2QC48_GOSRA_29730 and tr_A0A1U8MSQ0_A0A1U8MSQ0_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0D2TME3_A0A0D2TME3_GOSRA_29730 and tr_A0A1U8JFS6_A0A1U8JFS6_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0V1DD94_A0A0V1DD94_TRIBR_45882 and tr_A0A0V0WXB4_A0A0V0WXB4_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1DD94_A0A0V1DD94_TRIBR_45882 and tr_A0A0V1L009_A0A0V1L009_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1DD94_A0A0V1DD94_TRIBR_45882 and tr_A0A0V0TH54_A0A0V0TH54_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A164XFR6_A0A164XFR6_9HOMO_1314777 and tr_A0A166G5Z7_A0A166G5Z7_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S3ZF94_A0A1S3ZF94_TOBAC_4097 and tr_A0A1U7W629_A0A1U7W629_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1U8FCT9_A0A1U8FCT9_CAPAN_4072 and tr_A0A2G3BF85_A0A2G3BF85_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2I1GWN3_A0A2I1GWN3_9GLOM_588596 and tr_U9TAN1_U9TAN1_RHIID_747089 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_020621/phylogeny-snakemake/results/Q9UQ90/4_raxmlng_ancestral/Q9UQ90.raxml.reduced.phy

Alignment comprises 1 partitions and 795 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 795
Gaps: 16.25 %
Invariant sites: 3.77 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UQ90/4_raxmlng_ancestral/Q9UQ90.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_020621/phylogeny-snakemake/results/Q9UQ90/3_mltree/Q9UQ90.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 199 / 15920
[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: -322366.775142

[00:00:00 -322366.775142] Initial branch length optimization
[00:00:02 -317742.203102] Model parameter optimization (eps = 0.100000)

[00:00:48] Tree #1, final logLikelihood: -316630.467830


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.227050,0.175103) (0.233055,0.240217) (0.297378,1.049206) (0.242517,2.442089) 
   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_020621/phylogeny-snakemake/results/Q9UQ90/4_raxmlng_ancestral/Q9UQ90.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UQ90/4_raxmlng_ancestral/Q9UQ90.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UQ90/4_raxmlng_ancestral/Q9UQ90.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9UQ90/4_raxmlng_ancestral/Q9UQ90.raxml.log

Analysis started: 02-Jun-2021 14:58:08 / finished: 02-Jun-2021 14:59:03

Elapsed time: 55.269 seconds