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 12-Jul-2021 17:13:45 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/2_msa/Q01518_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/3_mltree/Q01518.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/4_raxmlng_ancestral/Q01518 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626099225
  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/300621_run/phylogeny-snakemake/results/Q01518/2_msa/Q01518_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 475 sites

WARNING: Sequences tr_J3K918_J3K918_COCIM_246410 and tr_A0A0J6YAH1_A0A0J6YAH1_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B8PBL3_B8PBL3_POSPM_561896 and tr_A0A1X6N854_A0A1X6N854_9APHY_670580 are exactly identical!
WARNING: Sequences tr_B8N6C9_B8N6C9_ASPFN_332952 and tr_Q2UCD3_Q2UCD3_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8N6C9_B8N6C9_ASPFN_332952 and tr_A0A0F0IEV0_A0A0F0IEV0_ASPPU_1403190 are exactly identical!
WARNING: Sequences tr_B8N6C9_B8N6C9_ASPFN_332952 and tr_A0A1S9DR54_A0A1S9DR54_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_B8N6C9_B8N6C9_ASPFN_332952 and tr_A0A2G7G2G3_A0A2G7G2G3_9EURO_656916 are exactly identical!
WARNING: Sequences tr_C6HFU8_C6HFU8_AJECH_544712 and tr_F0UMH6_F0UMH6_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A0E0ICN9_A0A0E0ICN9_ORYNI_4536 and tr_A2YVR2_A2YVR2_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A2QRC4_A2QRC4_ASPNC_425011 and tr_G3YHD6_G3YHD6_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QRC4_A2QRC4_ASPNC_425011 and tr_A0A319AN78_A0A319AN78_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_I1QJ48_I1QJ48_ORYGL_4538 and tr_A0A0D3H0W0_A0A0D3H0W0_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1QJ48_I1QJ48_ORYGL_4538 and tr_A0A0E0AW30_A0A0E0AW30_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_I1QJ48_I1QJ48_ORYGL_4538 and tr_Q6ZAC2_Q6ZAC2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G2YLB9_G2YLB9_BOTF4_999810 and tr_M7TJL0_M7TJL0_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SZ39_F2SZ39_TRIRC_559305 and tr_A0A178F498_A0A178F498_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_G7P4H5_G7P4H5_MACFA_9541 and tr_A0A2K6CQZ7_A0A2K6CQZ7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F2Q5F1_F2Q5F1_TRIEC_559882 and tr_A0A059JIS9_A0A059JIS9_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_A0A015LXW7_A0A015LXW7_9GLOM_1432141 and tr_A0A2I1G7D0_A0A2I1G7D0_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015LXW7_A0A015LXW7_9GLOM_1432141 and tr_A0A2H5T5J9_A0A2H5T5J9_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A096N1K2_A0A096N1K2_PAPAN_9555 and tr_A0A0D9S7N5_A0A0D9S7N5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096N1K2_A0A096N1K2_PAPAN_9555 and tr_A0A2K6CU40_A0A2K6CU40_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0F8WSE0_A0A0F8WSE0_9EURO_308745 and tr_A0A2T5M2J7_A0A2T5M2J7_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0V1D9Y5_A0A0V1D9Y5_TRIBR_45882 and tr_A0A0V1NH27_A0A0V1NH27_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1D9Y5_A0A0V1D9Y5_TRIBR_45882 and tr_A0A0V0U3L3_A0A0V0U3L3_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S4AVZ0_A0A1S4AVZ0_TOBAC_4097 and tr_A0A1U7W9D2_A0A1U7W9D2_NICSY_4096 are exactly identical!
WARNING: Duplicate sequences found: 25

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/4_raxmlng_ancestral/Q01518.raxml.reduced.phy

Alignment comprises 1 partitions and 475 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 475
Gaps: 11.35 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/4_raxmlng_ancestral/Q01518.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/300621_run/phylogeny-snakemake/results/Q01518/3_mltree/Q01518.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 119 / 9520
[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: -252276.526855

[00:00:00 -252276.526855] Initial branch length optimization
[00:00:01 -250800.478804] Model parameter optimization (eps = 0.100000)

[00:00:34] Tree #1, final logLikelihood: -249889.912379


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.170050,0.452466) (0.233985,0.488536) (0.270595,0.796362) (0.325370,1.823327) 
   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/300621_run/phylogeny-snakemake/results/Q01518/4_raxmlng_ancestral/Q01518.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/4_raxmlng_ancestral/Q01518.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/4_raxmlng_ancestral/Q01518.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/4_raxmlng_ancestral/Q01518.raxml.log

Analysis started: 12-Jul-2021 17:13:45 / finished: 12-Jul-2021 17:14:24

Elapsed time: 39.460 seconds

Consumed energy: 2.796 Wh