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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 03-Jun-2021 01:54:10 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13501/2_msa/Q13501_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13501/3_mltree/Q13501.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13501/4_raxmlng_ancestral/Q13501 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622674450
  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/020621_run/phylogeny-snakemake/results/Q13501/2_msa/Q13501_nogap_msa.fasta
[00:00:00] Loaded alignment with 810 taxa and 440 sites

WARNING: Sequences tr_E1BW48_E1BW48_CHICK_9031 and tr_U3I746_U3I746_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_E1BW48_E1BW48_CHICK_9031 and tr_A0A151NXF6_A0A151NXF6_ALLMI_8496 are exactly identical!
WARNING: Sequences sp_Q4U2R1_HERC2_MOUSE_10090 and tr_A0A0G2JUC9_A0A0G2JUC9_RAT_10116 are exactly identical!
WARNING: Sequences tr_B6QTK4_B6QTK4_TALMQ_441960 and tr_A0A093UPS0_A0A093UPS0_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2VRI5_B2VRI5_PYRTR_426418 and tr_A0A2W1GCT3_A0A2W1GCT3_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_B2WAC1_B2WAC1_PYRTR_426418 and tr_A0A2W1GPP7_A0A2W1GPP7_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_B8NV63_B8NV63_ASPFN_332952 and tr_Q2U568_Q2U568_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NV63_B8NV63_ASPFN_332952 and tr_A0A1S9DIF2_A0A1S9DIF2_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_E2RDC2_E2RDC2_CANLF_9615 and tr_F7AM44_F7AM44_HORSE_9796 are exactly identical!
WARNING: Sequences tr_E2RDC2_E2RDC2_CANLF_9615 and tr_A0A2U3W9Z2_A0A2U3W9Z2_ODORO_9708 are exactly identical!
WARNING: Sequences tr_H2R540_H2R540_PANTR_9598 and tr_A0A2R9B442_A0A2R9B442_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5Q2G3_W5Q2G3_SHEEP_9940 and tr_E1B782_E1B782_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_J4W6F2_J4W6F2_BEAB2_655819 and tr_A0A0A2VF79_A0A0A2VF79_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J4W6F2_J4W6F2_BEAB2_655819 and tr_A0A2N6NUY4_A0A2N6NUY4_BEABA_176275 are exactly identical!
WARNING: Sequences tr_A1DMD2_A1DMD2_NEOFI_331117 and tr_A0A0S7DLD5_A0A0S7DLD5_9EURO_293939 are exactly identical!
WARNING: Sequences tr_H0ZJQ4_H0ZJQ4_TAEGU_59729 and tr_U3JN73_U3JN73_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0ZJQ4_H0ZJQ4_TAEGU_59729 and tr_A0A091EHF1_A0A091EHF1_CORBR_85066 are exactly identical!
WARNING: Sequences tr_F9XBM3_F9XBM3_ZYMTI_336722 and tr_A0A1X7RTH9_A0A1X7RTH9_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YXS6_G2YXS6_BOTF4_999810 and tr_M7U883_M7U883_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SHV6_F2SHV6_TRIRC_559305 and tr_A0A178F063_A0A178F063_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_F2STK6_F2STK6_TRIRC_559305 and tr_D4APL1_D4APL1_ARTBC_663331 are exactly identical!
WARNING: Sequences tr_F2STK6_F2STK6_TRIRC_559305 and tr_A0A178EVZ6_A0A178EVZ6_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_B3S4E9_B3S4E9_TRIAD_10228 and tr_A0A369S314_A0A369S314_9METZ_287889 are exactly identical!
WARNING: Sequences tr_A0A015IS55_A0A015IS55_9GLOM_1432141 and tr_A0A2H5S9C9_A0A2H5S9C9_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015JLD6_A0A015JLD6_9GLOM_1432141 and tr_A0A2H5UEN5_A0A2H5UEN5_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A096N821_A0A096N821_PAPAN_9555 and tr_A0A2K6B053_A0A2K6B053_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0A1P4C8_A0A0A1P4C8_9FUNG_58291 and tr_A0A367K8C9_A0A367K8C9_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A091VRX9_A0A091VRX9_OPIHO_30419 and tr_A0A091GJE6_A0A091GJE6_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A091VRX9_A0A091VRX9_OPIHO_30419 and tr_A0A0A0A8M2_A0A0A0A8M2_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0MLM1_A0A2I0MLM1_COLLI_8932 and tr_A0A1V4JBE1_A0A1V4JBE1_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A2N5SMP0_A0A2N5SMP0_9BASI_200324 and tr_A0A2N5VP68_A0A2N5VP68_9BASI_200324 are exactly identical!
WARNING: Duplicate sequences found: 31

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13501/4_raxmlng_ancestral/Q13501.raxml.reduced.phy

Alignment comprises 1 partitions and 440 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 440
Gaps: 44.43 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13501/4_raxmlng_ancestral/Q13501.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/020621_run/phylogeny-snakemake/results/Q13501/3_mltree/Q13501.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 110 / 8800
[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: -214051.709390

[00:00:00 -214051.709390] Initial branch length optimization
[00:00:01 -186883.584100] Model parameter optimization (eps = 0.100000)

[00:00:28] Tree #1, final logLikelihood: -186471.457104


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.051856,0.135197) (0.054393,0.388960) (0.375189,0.721006) (0.518562,1.352430) 
   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/020621_run/phylogeny-snakemake/results/Q13501/4_raxmlng_ancestral/Q13501.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13501/4_raxmlng_ancestral/Q13501.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13501/4_raxmlng_ancestral/Q13501.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13501/4_raxmlng_ancestral/Q13501.raxml.log

Analysis started: 03-Jun-2021 01:54:10 / finished: 03-Jun-2021 01:54:41

Elapsed time: 31.563 seconds

Consumed energy: 2.719 Wh