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 12-Jul-2021 18:24:44 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95170/2_msa/O95170_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95170/3_mltree/O95170.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95170/4_raxmlng_ancestral/O95170 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626103484
  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/O95170/2_msa/O95170_nogap_msa.fasta
[00:00:00] Loaded alignment with 593 taxa and 752 sites

WARNING: Sequences tr_A0A0E1RYS0_A0A0E1RYS0_COCIM_246410 and tr_E9D894_E9D894_COCPS_443226 are exactly identical!
WARNING: Sequences tr_A0A179UPZ6_A0A179UPZ6_BLAGS_559298 and tr_C5GE15_C5GE15_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_C6HK03_C6HK03_AJECH_544712 and tr_F0UJJ6_F0UJJ6_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_M4A9Y8_M4A9Y8_XIPMA_8083 and tr_A0A087XX61_A0A087XX61_POEFO_48698 are exactly identical!
WARNING: Sequences sp_A2QCU8_SCONB_ASPNC_425011 and tr_G3Y308_G3Y308_ASPNA_380704 are exactly identical!
WARNING: Sequences sp_A2QCU8_SCONB_ASPNC_425011 and tr_A0A319BHW1_A0A319BHW1_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_H1A1C1_H1A1C1_TAEGU_59729 and tr_A0A091EW16_A0A091EW16_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H1A1C1_H1A1C1_TAEGU_59729 and tr_A0A091JJA7_A0A091JJA7_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_H1A1C1_H1A1C1_TAEGU_59729 and tr_A0A093PJ80_A0A093PJ80_9PASS_328815 are exactly identical!
WARNING: Sequences tr_H1A1C1_H1A1C1_TAEGU_59729 and tr_A0A091VAT2_A0A091VAT2_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_H1A1C1_H1A1C1_TAEGU_59729 and tr_A0A087R779_A0A087R779_APTFO_9233 are exactly identical!
WARNING: Sequences tr_H1A1C1_H1A1C1_TAEGU_59729 and tr_A0A093I007_A0A093I007_STRCA_441894 are exactly identical!
WARNING: Sequences tr_H1A1C1_H1A1C1_TAEGU_59729 and tr_A0A099YZN8_A0A099YZN8_TINGU_94827 are exactly identical!
WARNING: Sequences tr_H1A1C1_H1A1C1_TAEGU_59729 and tr_A0A0A0ABD7_A0A0A0ABD7_CHAVO_50402 are exactly identical!
WARNING: Sequences sp_Q5M786_WDR5_XENTR_8364 and tr_Q66J98_Q66J98_XENLA_8355 are exactly identical!
WARNING: Sequences tr_F2SL63_F2SL63_TRIRC_559305 and tr_A0A178ERT8_A0A178ERT8_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_A0A0D2XR52_A0A0D2XR52_FUSO4_426428 and tr_A0A0D2XTR7_A0A0D2XTR7_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_L0PDA0_L0PDA0_PNEJ8_1209962 and tr_A0A0W4ZPZ3_A0A0W4ZPZ3_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_A0A0V1D4Q0_A0A0V1D4Q0_TRIBR_45882 and tr_A0A0V1KYS5_A0A0V1KYS5_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1D4Q0_A0A0V1D4Q0_TRIBR_45882 and tr_A0A0V1PF94_A0A0V1PF94_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1D4Q0_A0A0V1D4Q0_TRIBR_45882 and tr_A0A0V0UJ95_A0A0V0UJ95_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0WZT4_A0A0V0WZT4_9BILA_92179 and tr_A0A0V0VIF8_A0A0V0VIF8_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0WZT4_A0A0V0WZT4_9BILA_92179 and tr_A0A0V1NTE2_A0A0V1NTE2_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1LSG9_A0A0V1LSG9_9BILA_6335 and tr_A0A0V0U5L2_A0A0V0U5L2_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S4AVG4_A0A1S4AVG4_TOBAC_4097 and tr_A0A1U7XG58_A0A1U7XG58_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2N5TJG5_A0A2N5TJG5_9BASI_200324 and tr_A0A2N5VSY8_A0A2N5VSY8_9BASI_200324 are exactly identical!
WARNING: Sequences tr_A0A2P5FH88_A0A2P5FH88_TREOI_63057 and tr_A0A2P5BIR8_A0A2P5BIR8_PARAD_3476 are exactly identical!
WARNING: Duplicate sequences found: 27

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/O95170/4_raxmlng_ancestral/O95170.raxml.reduced.phy

Alignment comprises 1 partitions and 752 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 752
Gaps: 48.99 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95170/4_raxmlng_ancestral/O95170.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/O95170/3_mltree/O95170.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 188 / 15040
[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: -218868.242844

[00:00:00 -218868.242844] Initial branch length optimization
[00:00:00 -216424.382960] Model parameter optimization (eps = 0.100000)

[00:00:34] Tree #1, final logLikelihood: -215801.190605


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.066702,0.375988) (0.110752,0.379040) (0.414453,0.759440) (0.408094,1.514823) 
   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/O95170/4_raxmlng_ancestral/O95170.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95170/4_raxmlng_ancestral/O95170.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95170/4_raxmlng_ancestral/O95170.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95170/4_raxmlng_ancestral/O95170.raxml.log

Analysis started: 12-Jul-2021 18:24:44 / finished: 12-Jul-2021 18:25:23

Elapsed time: 39.287 seconds

Consumed energy: 3.428 Wh