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 03-Jun-2021 02:15:06 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22557/2_msa/P22557_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22557/3_mltree/P22557.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22557/4_raxmlng_ancestral/P22557 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622675706
  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/P22557/2_msa/P22557_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 587 sites

WARNING: Sequences tr_J3K7B6_J3K7B6_COCIM_246410 and tr_A0A0J6Y3B8_A0A0J6Y3B8_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B2VUY5_B2VUY5_PYRTR_426418 and tr_A0A2W1FVV8_A0A2W1FVV8_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_A0A179UID6_A0A179UID6_BLAGS_559298 and tr_C5GAJ8_C5GAJ8_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_A0A2I3SJ87_A0A2I3SJ87_PANTR_9598 and tr_A0A2R8ZNC9_A0A2R8ZNC9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QMR0_H2QMR0_PANTR_9598 and sp_P13196_HEM1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QMR0_H2QMR0_PANTR_9598 and tr_A0A2R9CAD9_A0A2R9CAD9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FB86_F9FB86_FUSOF_660025 and tr_N4TYQ7_N4TYQ7_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FB86_F9FB86_FUSOF_660025 and tr_X0DC49_X0DC49_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FB86_F9FB86_FUSOF_660025 and tr_A0A2H3H7Z7_A0A2H3H7Z7_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_Q2UTR0_Q2UTR0_ASPOR_510516 and tr_Q9Y8A4_Q9Y8A4_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A2R9H8_A2R9H8_ASPNC_425011 and tr_G3Y4M1_G3Y4M1_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2R9H8_A2R9H8_ASPNC_425011 and tr_A0A319A6A5_A0A319A6A5_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F6VBC4_F6VBC4_MACMU_9544 and tr_G7Q2U5_G7Q2U5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6VBC4_F6VBC4_MACMU_9544 and tr_A0A096N168_A0A096N168_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6VBC4_F6VBC4_MACMU_9544 and tr_A0A2K6CGE0_A0A2K6CGE0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7XSH9_G7XSH9_ASPKW_1033177 and tr_A0A146FYL2_A0A146FYL2_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XSH9_G7XSH9_ASPKW_1033177 and tr_A0A1L9N523_A0A1L9N523_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_F4NZF8_F4NZF8_BATDJ_684364 and tr_A0A177WFC2_A0A177WFC2_BATDE_403673 are exactly identical!
WARNING: Sequences tr_G2XWX9_G2XWX9_BOTF4_999810 and tr_M7URJ4_M7URJ4_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_V2XX48_V2XX48_MONRO_1381753 and tr_A0A0W0FCA8_A0A0W0FCA8_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2RDE3_W2RDE3_PHYPN_761204 and tr_W2JYK1_W2JYK1_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A096NSF2_A0A096NSF2_PAPAN_9555 and tr_A0A2K5NY31_A0A2K5NY31_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NSF2_A0A096NSF2_PAPAN_9555 and tr_A0A2K5YJF4_A0A2K5YJF4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0F0I372_A0A0F0I372_ASPPU_1403190 and tr_A0A2G7FVU0_A0A2G7FVU0_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A0G0A1E4_A0A0G0A1E4_TRIHA_5544 and tr_A0A2T4AR31_A0A2T4AR31_TRIHA_983964 are exactly identical!
WARNING: Sequences tr_A0A164Z4Y4_A0A164Z4Y4_9HOMO_1314777 and tr_A0A166CNR1_A0A166CNR1_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S3LI09_A0A1S3LI09_SALSA_8030 and tr_C0HAP7_C0HAP7_SALSA_8030 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/020621_run/phylogeny-snakemake/results/P22557/4_raxmlng_ancestral/P22557.raxml.reduced.phy

Alignment comprises 1 partitions and 587 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 587
Gaps: 17.57 %
Invariant sites: 1.19 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22557/4_raxmlng_ancestral/P22557.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/P22557/3_mltree/P22557.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 147 / 11760
[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: -222942.737305

[00:00:00 -222942.737305] Initial branch length optimization
[00:00:01 -217759.482341] Model parameter optimization (eps = 0.100000)

[00:00:41] Tree #1, final logLikelihood: -217273.794355


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.212417,0.169931) (0.222015,0.274890) (0.237812,0.828882) (0.327757,2.153293) 
   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/P22557/4_raxmlng_ancestral/P22557.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22557/4_raxmlng_ancestral/P22557.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22557/4_raxmlng_ancestral/P22557.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22557/4_raxmlng_ancestral/P22557.raxml.log

Analysis started: 03-Jun-2021 02:15:06 / finished: 03-Jun-2021 02:15:54

Elapsed time: 47.761 seconds

Consumed energy: 3.294 Wh