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 17:21:27 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/2_msa/Q7RTP6_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/3_mltree/Q7RTP6.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/4_raxmlng_ancestral/Q7RTP6 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626099687
  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/Q7RTP6/2_msa/Q7RTP6_nogap_msa.fasta
[00:00:00] Loaded alignment with 972 taxa and 2002 sites

WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_U3IMX5_U3IMX5_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_K7CTI8_K7CTI8_PANTR_9598 and tr_A0A2R8ZU41_A0A2R8ZU41_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A158NF25_A0A158NF25_ATTCE_12957 and tr_A0A195AUX5_A0A195AUX5_9HYME_520822 are exactly identical!
WARNING: Sequences tr_G7PQP9_G7PQP9_MACFA_9541 and tr_A0A2K5P755_A0A2K5P755_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7PQP9_G7PQP9_MACFA_9541 and tr_A0A2K6CGD9_A0A2K6CGD9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PQP9_G7PQP9_MACFA_9541 and tr_A0A2K6AI94_A0A2K6AI94_MANLE_9568 are exactly identical!
WARNING: Sequences sp_F1MF74_MICA2_BOVIN_9913 and tr_H9GW33_H9GW33_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_L0P961_L0P961_PNEJ8_1209962 and tr_A0A0W4ZTP2_A0A0W4ZTP2_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_W2QC39_W2QC39_PHYPN_761204 and tr_W2LBL6_W2LBL6_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2QIL9_W2QIL9_PHYPN_761204 and tr_A0A0W8DJ24_A0A0W8DJ24_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A059IXW0_A0A059IXW0_9EURO_1215338 and tr_A0A178F4W9_A0A178F4W9_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_A0A094EK08_A0A094EK08_9PEZI_1420912 and tr_A0A1B8GA32_A0A1B8GA32_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0V1P1R2_A0A0V1P1R2_9BILA_92180 and tr_A0A0V0U8Q0_A0A0V0U8Q0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A2D0RIB7_A0A2D0RIB7_ICTPU_7998 and tr_A0A2D0RIC0_A0A2D0RIC0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RIB7_A0A2D0RIB7_ICTPU_7998 and tr_A0A2D0RIC2_A0A2D0RIC2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RIB7_A0A2D0RIB7_ICTPU_7998 and tr_A0A2D0RJF6_A0A2D0RJF6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RIB7_A0A2D0RIB7_ICTPU_7998 and tr_A0A2D0RK17_A0A2D0RK17_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RIB7_A0A2D0RIB7_ICTPU_7998 and tr_A0A2D0RK22_A0A2D0RK22_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RTA7_A0A2D0RTA7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RTB4_A0A2D0RTB4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RTB9_A0A2D0RTB9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RU88_A0A2D0RU88_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RU96_A0A2D0RU96_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RUU7_A0A2D0RUU7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RUV1_A0A2D0RUV1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RUV6_A0A2D0RUV6_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 26

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/Q7RTP6/4_raxmlng_ancestral/Q7RTP6.raxml.reduced.phy

Alignment comprises 1 partitions and 2002 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 2002
Gaps: 60.75 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/4_raxmlng_ancestral/Q7RTP6.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/Q7RTP6/3_mltree/Q7RTP6.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 501 / 40080
[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: -659934.667414

[00:00:00 -659934.667414] Initial branch length optimization
[00:00:07 -554439.553070] Model parameter optimization (eps = 0.100000)

[00:02:50] Tree #1, final logLikelihood: -551291.448842


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.136054,0.383540) (0.078631,0.711808) (0.254723,0.579840) (0.530592,1.402489) 
   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/Q7RTP6/4_raxmlng_ancestral/Q7RTP6.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/4_raxmlng_ancestral/Q7RTP6.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/4_raxmlng_ancestral/Q7RTP6.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/4_raxmlng_ancestral/Q7RTP6.raxml.log

Analysis started: 12-Jul-2021 17:21:27 / finished: 12-Jul-2021 17:24:37

Elapsed time: 189.504 seconds

Consumed energy: 13.070 Wh