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 13:39:56 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20794/2_msa/P20794_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20794/3_mltree/P20794.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20794/4_raxmlng_ancestral/P20794 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622803196
  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/P20794/2_msa/P20794_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 623 sites

WARNING: Sequences tr_J3KEV7_J3KEV7_COCIM_246410 and tr_E9DF53_E9DF53_COCPS_443226 are exactly identical!
WARNING: Sequences tr_J3KEV7_J3KEV7_COCIM_246410 and tr_A0A0J6YC19_A0A0J6YC19_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QC23_B6QC23_TALMQ_441960 and tr_A0A093V9K0_A0A093V9K0_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2VSY1_B2VSY1_PYRTR_426418 and tr_A0A2W1DG04_A0A2W1DG04_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_D8RYZ9_D8RYZ9_SELML_88036 and tr_D8SV47_D8SV47_SELML_88036 are exactly identical!
WARNING: Sequences tr_Q1K5L2_Q1K5L2_NEUCR_367110 and tr_G4UTN4_G4UTN4_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_K7BPI4_K7BPI4_PANTR_9598 and tr_A0A2R9BLU7_A0A2R9BLU7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FWL9_F9FWL9_FUSOF_660025 and tr_N4UE36_N4UE36_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FWL9_F9FWL9_FUSOF_660025 and tr_X0CME9_X0CME9_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_J4UVF0_J4UVF0_BEAB2_655819 and tr_A0A0A2WGN1_A0A0A2WGN1_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_Q2UFB4_Q2UFB4_ASPOR_510516 and tr_A0A1S9E0Y2_A0A1S9E0Y2_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A0E0HK28_A0A0E0HK28_ORYNI_4536 and tr_A0A0E0PSP6_A0A0E0PSP6_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0HK28_A0A0E0HK28_ORYNI_4536 and tr_A0A0D3GC28_A0A0D3GC28_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A2QC16_A2QC16_ASPNC_425011 and tr_G3Y1S0_G3Y1S0_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QC16_A2QC16_ASPNC_425011 and tr_A0A319B677_A0A319B677_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F7GEP8_F7GEP8_MACMU_9544 and tr_A0A2K5NHW3_A0A2K5NHW3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7GEP8_F7GEP8_MACMU_9544 and tr_A0A2K6C216_A0A2K6C216_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7GEP8_F7GEP8_MACMU_9544 and tr_A0A2K5XE98_A0A2K5XE98_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7X698_G7X698_ASPKW_1033177 and tr_A0A146FL30_A0A146FL30_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A0A0D2YBY3_A0A0D2YBY3_FUSO4_426428 and tr_A0A2H3GLY2_A0A2H3GLY2_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A0D2YBY3_A0A0D2YBY3_FUSO4_426428 and tr_A0A365NGV7_A0A365NGV7_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_W2PFI2_W2PFI2_PHYPN_761204 and tr_A0A0W8DZX9_A0A0W8DZX9_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PFI2_W2PFI2_PHYPN_761204 and tr_W2M6M6_W2M6M6_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2PPZ8_W2PPZ8_PHYPN_761204 and tr_A0A0W8D5F6_A0A0W8D5F6_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PPZ8_W2PPZ8_PHYPN_761204 and tr_W2MMW1_W2MMW1_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A067DTT7_A0A067DTT7_CITSI_2711 and tr_V4UBA2_V4UBA2_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A1S3WY48_A0A1S3WY48_TOBAC_4097 and tr_A0A1U7XLG1_A0A1U7XLG1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3Z017_A0A1S3Z017_TOBAC_4097 and tr_A0A1U7V4R6_A0A1U7V4R6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3ZY46_A0A1S3ZY46_TOBAC_4097 and tr_A0A1U7VE99_A0A1U7VE99_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A3Q0F7R8_A0A3Q0F7R8_VIGRR_3916 and tr_A0A3Q0F8A3_A0A3Q0F8A3_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A2V5IMP8_A0A2V5IMP8_9EURO_1450541 and tr_A0A2V5HSX5_A0A2V5HSX5_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 31

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/P20794/4_raxmlng_ancestral/P20794.raxml.reduced.phy

Alignment comprises 1 partitions and 623 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 623
Gaps: 28.22 %
Invariant sites: 0.64 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20794/4_raxmlng_ancestral/P20794.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/P20794/3_mltree/P20794.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 156 / 12480
[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: -267638.642372

[00:00:00 -267638.642372] Initial branch length optimization
[00:00:01 -235485.011382] Model parameter optimization (eps = 0.100000)

[00:00:47] Tree #1, final logLikelihood: -234821.351213


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.101731,0.155458) (0.151513,0.188543) (0.234898,0.623636) (0.511858,1.580766) 
   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/P20794/4_raxmlng_ancestral/P20794.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20794/4_raxmlng_ancestral/P20794.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20794/4_raxmlng_ancestral/P20794.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20794/4_raxmlng_ancestral/P20794.raxml.log

Analysis started: 04-Jun-2021 13:39:56 / finished: 04-Jun-2021 13:40:49

Elapsed time: 52.928 seconds