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 04-Jun-2021 14:18:33 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P25440/2_msa/P25440_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P25440/3_mltree/P25440.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P25440/4_raxmlng_ancestral/P25440 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622805513
  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_020621/phylogeny-snakemake/results/P25440/2_msa/P25440_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 801 sites

WARNING: Sequences tr_J3KJ91_J3KJ91_COCIM_246410 and tr_A0A0J6Y328_A0A0J6Y328_COCIT_404692 are exactly identical!
WARNING: Sequences tr_D8R369_D8R369_SELML_88036 and tr_D8TC92_D8TC92_SELML_88036 are exactly identical!
WARNING: Sequences tr_A0A2I2Y8Z2_A0A2I2Y8Z2_GORGO_9595 and sp_P25440_BRD2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_B8N0X6_B8N0X6_ASPFN_332952 and tr_A0A1S9DLC1_A0A1S9DLC1_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UHG2_A0A179UHG2_BLAGS_559298 and tr_A0A179U4K4_A0A179U4K4_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_A0A2I3TJ11_A0A2I3TJ11_PANTR_9598 and sp_O60885_BRD4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F7G2U9_F7G2U9_MACMU_9544 and tr_A0A2K5MTF8_A0A2K5MTF8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7G2U9_F7G2U9_MACMU_9544 and tr_A0A2K6C400_A0A2K6C400_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2K1KP36_A0A2K1KP36_PHYPA_3218 and tr_A0A2K1KP47_A0A2K1KP47_PHYPA_3218 are exactly identical!
WARNING: Sequences tr_G7X880_G7X880_ASPKW_1033177 and tr_A0A146FKW4_A0A146FKW4_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A0A015IYF5_A0A015IYF5_9GLOM_1432141 and tr_A0A2H5RQ40_A0A2H5RQ40_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2I3MN57_A0A2I3MN57_PAPAN_9555 and tr_A0A2K5MC37_A0A2K5MC37_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3MN57_A0A2I3MN57_PAPAN_9555 and tr_A0A2K6A8M8_A0A2K6A8M8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0F0IHV0_A0A0F0IHV0_ASPPU_1403190 and tr_A0A2G7EPK4_A0A2G7EPK4_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A2I0M3Q8_A0A2I0M3Q8_COLLI_8932 and tr_A0A1V4J652_A0A1V4J652_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A100IBB2_A0A100IBB2_ASPNG_5061 and tr_A0A1L9MVK6_A0A1L9MVK6_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1S3ZWA3_A0A1S3ZWA3_TOBAC_4097 and tr_A0A1U7YX65_A0A1U7YX65_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1R1XQB5_A0A1R1XQB5_9FUNG_133412 and tr_A0A1R1XWH4_A0A1R1XWH4_9FUNG_133412 are exactly identical!
WARNING: Sequences tr_A0A226MCM5_A0A226MCM5_CALSU_9009 and tr_A0A226P4V3_A0A226P4V3_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0PRC2_A0A2D0PRC2_ICTPU_7998 and tr_W5U5R8_W5U5R8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PU48_A0A2D0PU48_ICTPU_7998 and tr_A0A2D0PU53_A0A2D0PU53_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PU48_A0A2D0PU48_ICTPU_7998 and tr_A0A2D0PVK0_A0A2D0PVK0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PU48_A0A2D0PU48_ICTPU_7998 and tr_A0A2D0PVL7_A0A2D0PVL7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PU48_A0A2D0PU48_ICTPU_7998 and tr_A0A2D0PXB0_A0A2D0PXB0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PU48_A0A2D0PU48_ICTPU_7998 and tr_A0A2D0PY73_A0A2D0PY73_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RXX7_A0A2D0RXX7_ICTPU_7998 and tr_W5UFH2_W5UFH2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2V5J8W1_A0A2V5J8W1_9EURO_1450541 and tr_A0A2V5HDW2_A0A2V5HDW2_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 27

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P25440/4_raxmlng_ancestral/P25440.raxml.reduced.phy

Alignment comprises 1 partitions and 801 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 801
Gaps: 34.40 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P25440/4_raxmlng_ancestral/P25440.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_020621/phylogeny-snakemake/results/P25440/3_mltree/P25440.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 201 / 16080
[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: -324876.439301

[00:00:00 -324876.439301] Initial branch length optimization
[00:00:01 -303271.355808] Model parameter optimization (eps = 0.100000)

[00:01:22] Tree #1, final logLikelihood: -302429.976654


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.132464,2.533970) (0.087381,0.132343) (0.251165,0.424531) (0.528989,1.032437) 
   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_020621/phylogeny-snakemake/results/P25440/4_raxmlng_ancestral/P25440.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P25440/4_raxmlng_ancestral/P25440.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P25440/4_raxmlng_ancestral/P25440.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P25440/4_raxmlng_ancestral/P25440.raxml.log

Analysis started: 04-Jun-2021 14:18:33 / finished: 04-Jun-2021 14:20:02

Elapsed time: 89.251 seconds