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 02-Jun-2021 18:20:53 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UGJ0/2_msa/Q9UGJ0_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UGJ0/3_mltree/Q9UGJ0.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UGJ0/4_raxmlng_ancestral/Q9UGJ0 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622647253
  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/Q9UGJ0/2_msa/Q9UGJ0_nogap_msa.fasta
[00:00:00] Loaded alignment with 1000 taxa and 569 sites

WARNING: Sequences tr_B6HLM4_B6HLM4_PENRW_500485 and tr_K9G2Z9_K9G2Z9_PEND2_1170229 are exactly identical!
WARNING: Sequences tr_B6HLM4_B6HLM4_PENRW_500485 and tr_W6Q8N5_W6Q8N5_PENRF_1365484 are exactly identical!
WARNING: Sequences tr_B6HLM4_B6HLM4_PENRW_500485 and tr_A0A0M8NY15_A0A0M8NY15_9EURO_229535 are exactly identical!
WARNING: Sequences tr_B6HLM4_B6HLM4_PENRW_500485 and tr_A0A1V6R222_A0A1V6R222_9EURO_60172 are exactly identical!
WARNING: Sequences tr_B6Q695_B6Q695_TALMQ_441960 and tr_A0A093VGD8_A0A093VGD8_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_H2NH63_H2NH63_PONAB_9601 and tr_H9EQE8_H9EQE8_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2NH63_H2NH63_PONAB_9601 and tr_A0A096MQF5_A0A096MQF5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2NH63_H2NH63_PONAB_9601 and tr_A0A0D9R1J8_A0A0D9R1J8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2NH63_H2NH63_PONAB_9601 and tr_A0A2K6BZA8_A0A2K6BZA8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_V5ILJ9_V5ILJ9_NEUCR_367110 and tr_G4UHH4_G4UHH4_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_A0A179UYW1_A0A179UYW1_BLAGS_559298 and tr_C5GL51_C5GL51_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_A0A2I3TVR3_A0A2I3TVR3_PANTR_9598 and tr_A0A2R9C3Z4_A0A2R9C3Z4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9G8J8_F9G8J8_FUSOF_660025 and tr_N4UNL9_N4UNL9_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9G8J8_F9G8J8_FUSOF_660025 and tr_X0CXG1_X0CXG1_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9G8J8_F9G8J8_FUSOF_660025 and tr_A0A2H3GIJ3_A0A2H3GIJ3_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_E9D2L6_E9D2L6_COCPS_443226 and tr_A0A0J6YMG2_A0A0J6YMG2_COCIT_404692 are exactly identical!
WARNING: Sequences tr_M3ZIH8_M3ZIH8_XIPMA_8083 and tr_A0A096M3D7_A0A096M3D7_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A2R415_A2R415_ASPNC_425011 and tr_A0A317UZ95_A0A317UZ95_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A2R415_A2R415_ASPNC_425011 and tr_A0A319ARF7_A0A319ARF7_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A0A1D5R5V9_A0A1D5R5V9_MACMU_9544 and tr_A0A096NE17_A0A096NE17_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5R5V9_A0A1D5R5V9_MACMU_9544 and tr_A0A2K5NPX5_A0A2K5NPX5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5R5V9_A0A1D5R5V9_MACMU_9544 and tr_A0A2K6D1J8_A0A2K6D1J8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6TF76_F6TF76_MACMU_9544 and tr_G7PK29_G7PK29_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6TF76_F6TF76_MACMU_9544 and tr_A0A2K6CWP4_A0A2K6CWP4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F9X2N8_F9X2N8_ZYMTI_336722 and tr_A0A1X7RIV9_A0A1X7RIV9_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YQX5_G2YQX5_BOTF4_999810 and tr_M7TWZ2_M7TWZ2_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_L0PBL3_L0PBL3_PNEJ8_1209962 and tr_A0A0W4ZWH5_A0A0W4ZWH5_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_A0A2I2UK65_A0A2I2UK65_FELCA_9685 and tr_A0A2U3Z8L1_A0A2U3Z8L1_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M2TV27_M2TV27_COCH5_701091 and tr_W6ZAQ5_W6ZAQ5_COCMI_930090 are exactly identical!
WARNING: Sequences tr_W2RD55_W2RD55_PHYPN_761204 and tr_W2J811_W2J811_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015N4P2_A0A015N4P2_9GLOM_1432141 and tr_A0A2H5SYJ8_A0A2H5SYJ8_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A078GBB2_A0A078GBB2_BRANA_3708 and tr_A0A0D3DYC3_A0A0D3DYC3_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0A0KHE6_A0A0A0KHE6_CUCSA_3659 and tr_A0A1S3C818_A0A1S3C818_CUCME_3656 are exactly identical!
WARNING: Sequences tr_A0A0V1CAM3_A0A0V1CAM3_TRIBR_45882 and tr_A0A0V1NKG3_A0A0V1NKG3_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A135LED5_A0A135LED5_PENPA_5078 and tr_A0A1V6S911_A0A1V6S911_9EURO_29845 are exactly identical!
WARNING: Sequences tr_A0A164XFB3_A0A164XFB3_9HOMO_1314777 and tr_A0A166G6H8_A0A166G6H8_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1V4KNC3_A0A1V4KNC3_PATFA_372326 and tr_A0A218UXF0_A0A218UXF0_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A2H3C7F5_A0A2H3C7F5_9AGAR_1076256 and tr_A0A284RAB3_A0A284RAB3_9AGAR_47428 are exactly identical!
WARNING: Sequences tr_A0A2Y9N005_A0A2Y9N005_DELLE_9749 and tr_A0A2Y9ERJ1_A0A2Y9ERJ1_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 39

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/Q9UGJ0/4_raxmlng_ancestral/Q9UGJ0.raxml.reduced.phy

Alignment comprises 1 partitions and 569 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 569
Gaps: 37.80 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UGJ0/4_raxmlng_ancestral/Q9UGJ0.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/Q9UGJ0/3_mltree/Q9UGJ0.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 143 / 11440
[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: -196094.154169

[00:00:00 -196094.154169] Initial branch length optimization
[00:00:02 -183093.061429] Model parameter optimization (eps = 0.100000)

[00:01:02] Tree #1, final logLikelihood: -182058.584636


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.165324,0.282838) (0.115345,0.232342) (0.256810,0.560182) (0.462521,1.691989) 
   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/Q9UGJ0/4_raxmlng_ancestral/Q9UGJ0.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UGJ0/4_raxmlng_ancestral/Q9UGJ0.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UGJ0/4_raxmlng_ancestral/Q9UGJ0.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UGJ0/4_raxmlng_ancestral/Q9UGJ0.raxml.log

Analysis started: 02-Jun-2021 18:20:53 / finished: 02-Jun-2021 18:22:00

Elapsed time: 67.125 seconds

Consumed energy: 5.860 Wh