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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 17-Jul-2021 07:22:27 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MD39/2_msa/B5MD39_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MD39/3_mltree/B5MD39.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MD39/4_raxmlng_ancestral/B5MD39 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626495747
  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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MD39/2_msa/B5MD39_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 225 sites

WARNING: Sequences tr_A0A0E1RWE4_A0A0E1RWE4_COCIM_246410 and tr_A0A0J6Y736_A0A0J6Y736_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QE90_B6QE90_TALMQ_441960 and tr_A0A093Y2G6_A0A093Y2G6_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_Q29G10_Q29G10_DROPS_46245 and tr_B4H7H9_B4H7H9_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B8MW63_B8MW63_ASPFN_332952 and tr_A0A0F0I1R7_A0A0F0I1R7_ASPPU_1403190 are exactly identical!
WARNING: Sequences tr_A0A179UY86_A0A179UY86_BLAGS_559298 and tr_C5GCI2_C5GCI2_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_A0A2J8IZQ0_A0A2J8IZQ0_PANTR_9598 and sp_P19440_GGT1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F9G5X4_F9G5X4_FUSOF_660025 and tr_A0A0D2Y927_A0A0D2Y927_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9G5X4_F9G5X4_FUSOF_660025 and tr_N4UCL2_N4UCL2_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9G5X4_F9G5X4_FUSOF_660025 and tr_X0CG17_X0CG17_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9G5X4_F9G5X4_FUSOF_660025 and tr_A0A2H3U389_A0A2H3U389_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9G5X4_F9G5X4_FUSOF_660025 and tr_A0A2H3GKR6_A0A2H3GKR6_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A0E0H1M5_A0A0E0H1M5_ORYNI_4536 and tr_A2XU68_A2XU68_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0H1M5_A0A0E0H1M5_ORYNI_4536 and tr_A0A0D9ZLM5_A0A0D9ZLM5_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0H1M5_A0A0E0H1M5_ORYNI_4536 and tr_A0A0P0WAX0_A0A0P0WAX0_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A2R1I0_A2R1I0_ASPNC_425011 and tr_A0A319AJC2_A0A319AJC2_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_H9H2T4_H9H2T4_MACMU_9544 and tr_A0A096NW57_A0A096NW57_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7XRQ6_G7XRQ6_ASPKW_1033177 and tr_A0A146F3F5_A0A146F3F5_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_I1PLV4_I1PLV4_ORYGL_4538 and tr_A0A0D3FWK8_A0A0D3FWK8_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_M4EXU2_M4EXU2_BRARP_51351 and tr_A0A078IT38_A0A078IT38_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4EXU3_M4EXU3_BRARP_51351 and tr_A0A078ITP2_A0A078ITP2_BRANA_3708 are exactly identical!
WARNING: Sequences tr_V2X522_V2X522_MONRO_1381753 and tr_A0A0W0F0S3_A0A0W0F0S3_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A015IUX8_A0A015IUX8_9GLOM_1432141 and tr_A0A2H5UGU2_A0A2H5UGU2_RHIID_747089 are exactly identical!
WARNING: Sequences tr_U4UJX4_U4UJX4_DENPD_77166 and tr_U4ULR6_U4ULR6_DENPD_77166 are exactly identical!
WARNING: Sequences tr_A0A0V0SFU3_A0A0V0SFU3_9BILA_6336 and tr_A0A0V1DGX8_A0A0V1DGX8_TRIBR_45882 are exactly identical!
WARNING: Sequences tr_A0A0V0SFU3_A0A0V0SFU3_9BILA_6336 and tr_A0A0V0X3S3_A0A0V0X3S3_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V0SFU3_A0A0V0SFU3_9BILA_6336 and tr_A0A0V0VXF8_A0A0V0VXF8_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0SFU3_A0A0V0SFU3_9BILA_6336 and tr_A0A0V1LLH4_A0A0V1LLH4_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0SFU3_A0A0V0SFU3_9BILA_6336 and tr_A0A0V1PJ73_A0A0V1PJ73_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0SFU3_A0A0V0SFU3_9BILA_6336 and tr_A0A0V0UI78_A0A0V0UI78_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1N7A4_A0A0V1N7A4_9BILA_268474 and tr_A0A0V1I971_A0A0V1I971_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A194VV02_A0A194VV02_9PEZI_105487 and tr_A0A194UNI3_A0A194UNI3_9PEZI_694573 are exactly identical!
WARNING: Sequences tr_A0A1S3ZPX3_A0A1S3ZPX3_TOBAC_4097 and tr_A0A1U7VUP5_A0A1U7VUP5_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1R1X452_A0A1R1X452_9FUNG_133412 and tr_A0A1R1XGM3_A0A1R1XGM3_9FUNG_133412 are exactly identical!
WARNING: Sequences tr_A0A2G2YUZ0_A0A2G2YUZ0_CAPAN_4072 and tr_A0A2G3BNX4_A0A2G3BNX4_CAPCH_80379 are exactly identical!
WARNING: Duplicate sequences found: 34

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MD39/4_raxmlng_ancestral/B5MD39.raxml.reduced.phy

Alignment comprises 1 partitions and 225 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 225
Gaps: 4.33 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MD39/4_raxmlng_ancestral/B5MD39.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MD39/3_mltree/B5MD39.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 57 / 4560
[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: -145828.166771

[00:00:00 -145828.166771] Initial branch length optimization
[00:00:01 -144476.902769] Model parameter optimization (eps = 0.100000)

[00:00:21] Tree #1, final logLikelihood: -143830.620337


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.196851,0.371758) (0.239811,0.450364) (0.348814,0.995977) (0.214524,2.197452) 
   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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MD39/4_raxmlng_ancestral/B5MD39.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MD39/4_raxmlng_ancestral/B5MD39.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MD39/4_raxmlng_ancestral/B5MD39.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MD39/4_raxmlng_ancestral/B5MD39.raxml.log

Analysis started: 17-Jul-2021 07:22:27 / finished: 17-Jul-2021 07:22:50

Elapsed time: 23.212 seconds