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 02-Jun-2021 18:27:34 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10515/2_msa/P10515_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10515/3_mltree/P10515.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10515/4_raxmlng_ancestral/P10515 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622647654
  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/P10515/2_msa/P10515_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 647 sites

WARNING: Sequences tr_B2W5N6_B2W5N6_PYRTR_426418 and tr_A0A2W1G8A5_A0A2W1G8A5_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_B8MX81_B8MX81_ASPFN_332952 and tr_A0A1S9DW28_A0A1S9DW28_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179USP9_A0A179USP9_BLAGS_559298 and tr_C5GDR2_C5GDR2_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9F373_F9F373_FUSOF_660025 and tr_A0A2H3TXX5_A0A2H3TXX5_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A2QMI1_A2QMI1_ASPNC_425011 and tr_A0A319AQH9_A0A319AQH9_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F6ZQ28_F6ZQ28_MACMU_9544 and tr_A0A096N7S5_A0A096N7S5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6ZQ28_F6ZQ28_MACMU_9544 and tr_A0A2K6BI72_A0A2K6BI72_MACNE_9545 are exactly identical!
WARNING: Sequences tr_I1PYR8_I1PYR8_ORYGL_4538 and tr_Q5VS74_Q5VS74_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0N8K7_A0A0E0N8K7_ORYRU_4529 and tr_Q6YPG2_Q6YPG2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0PSE9_A0A0E0PSE9_ORYRU_4529 and tr_A0A0D3GBU3_A0A0D3GBU3_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_E3LTJ2_E3LTJ2_CAERE_31234 and tr_A0A260ZTU5_A0A260ZTU5_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_F2SM07_F2SM07_TRIRC_559305 and tr_F2Q3F9_F2Q3F9_TRIEC_559882 are exactly identical!
WARNING: Sequences tr_F2SM07_F2SM07_TRIRC_559305 and tr_A0A178ER28_A0A178ER28_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_A0A0D2Y5A7_A0A0D2Y5A7_FUSO4_426428 and tr_N4UV30_N4UV30_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_A0A0D2Y5A7_A0A0D2Y5A7_FUSO4_426428 and tr_X0D6P0_X0D6P0_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0D2Y5A7_A0A0D2Y5A7_FUSO4_426428 and tr_A0A2H3GF02_A0A2H3GF02_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_M4EXB0_M4EXB0_BRARP_51351 and tr_A0A078GCX3_A0A078GCX3_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M7Z0L6_M7Z0L6_TRIUA_4572 and tr_A0A3B6R751_A0A3B6R751_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_V2XGI8_V2XGI8_MONRO_1381753 and tr_A0A0W0G2Q0_A0A0W0G2Q0_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A094EKG2_A0A094EKG2_9PEZI_1420912 and tr_A0A1B8GWX4_A0A1B8GWX4_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_V4SPV4_V4SPV4_9ROSI_85681 and tr_A0A2H5QBS8_A0A2H5QBS8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0F0I2A0_A0A0F0I2A0_ASPPU_1403190 and tr_A0A2G7FZY6_A0A2G7FZY6_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A0F8WEV6_A0A0F8WEV6_9EURO_308745 and tr_A0A2T5LNM1_A0A2T5LNM1_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0V0W5E5_A0A0V0W5E5_9BILA_92179 and tr_A0A0V1KWH8_A0A0V1KWH8_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0W5E5_A0A0V0W5E5_9BILA_92179 and tr_A0A0V0TQQ9_A0A0V0TQQ9_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S4C175_A0A1S4C175_TOBAC_4097 and tr_A0A1U7X4P1_A0A1U7X4P1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1U8F4C0_A0A1U8F4C0_CAPAN_4072 and tr_A0A2G3B0Z4_A0A2G3B0Z4_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2V5J215_A0A2V5J215_9EURO_1450541 and tr_A0A2V5HES8_A0A2V5HES8_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 28

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/P10515/4_raxmlng_ancestral/P10515.raxml.reduced.phy

Alignment comprises 1 partitions and 647 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 647
Gaps: 30.79 %
Invariant sites: 0.62 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10515/4_raxmlng_ancestral/P10515.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/P10515/3_mltree/P10515.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 162 / 12960
[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: -224263.331969

[00:00:00 -224263.331969] Initial branch length optimization
[00:00:01 -223791.256572] Model parameter optimization (eps = 0.100000)

[00:00:38] Tree #1, final logLikelihood: -223238.407552


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.186134,0.228850) (0.216392,0.335123) (0.251519,0.907547) (0.345955,1.897991) 
   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/P10515/4_raxmlng_ancestral/P10515.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10515/4_raxmlng_ancestral/P10515.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10515/4_raxmlng_ancestral/P10515.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10515/4_raxmlng_ancestral/P10515.raxml.log

Analysis started: 02-Jun-2021 18:27:34 / finished: 02-Jun-2021 18:28:19

Elapsed time: 44.865 seconds

Consumed energy: 2.645 Wh