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 02-Jun-2021 22:50:16 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43933/2_msa/O43933_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43933/3_mltree/O43933.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43933/4_raxmlng_ancestral/O43933 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622663416
  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/O43933/2_msa/O43933_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1283 sites

WARNING: Sequences tr_J3K3M5_J3K3M5_COCIM_246410 and tr_A0A0J7B7H5_A0A0J7B7H5_COCIT_404692 are exactly identical!
WARNING: Sequences tr_U9W4Q2_U9W4Q2_NEUCR_367110 and tr_G4URM7_G4URM7_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_A0A179UXY6_A0A179UXY6_BLAGS_559298 and tr_C5GR16_C5GR16_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9GFG6_F9GFG6_FUSOF_660025 and tr_X0D0C0_X0D0C0_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9GFG6_F9GFG6_FUSOF_660025 and tr_A0A2H3T5A0_A0A2H3T5A0_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_E9ETY2_E9ETY2_METRA_655844 and tr_A0A0D9NS03_A0A0D9NS03_METAN_1291518 are exactly identical!
WARNING: Sequences tr_C6HBG1_C6HBG1_AJECH_544712 and tr_F0UC53_F0UC53_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_Q2U021_Q2U021_ASPOR_510516 and tr_A0A1S9DDI8_A0A1S9DDI8_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A2QK32_A2QK32_ASPNC_425011 and tr_G7XVQ6_G7XVQ6_ASPKW_1033177 are exactly identical!
WARNING: Sequences tr_A2QK32_A2QK32_ASPNC_425011 and tr_G3YAG9_G3YAG9_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QK32_A2QK32_ASPNC_425011 and tr_A0A124BW77_A0A124BW77_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_A2QK32_A2QK32_ASPNC_425011 and tr_A0A1L9MUX0_A0A1L9MUX0_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A2QK32_A2QK32_ASPNC_425011 and tr_A0A1L9U660_A0A1L9U660_9EURO_767769 are exactly identical!
WARNING: Sequences tr_A2QK32_A2QK32_ASPNC_425011 and tr_A0A317V984_A0A317V984_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A2QK32_A2QK32_ASPNC_425011 and tr_A0A319A2A9_A0A319A2A9_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A2R7V4_A2R7V4_ASPNC_425011 and tr_G3Y653_G3Y653_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2R7V4_A2R7V4_ASPNC_425011 and tr_A0A319B3X9_A0A319B3X9_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XCW7_G7XCW7_ASPKW_1033177 and tr_A0A146FFF0_A0A146FFF0_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A2XCL6_A2XCL6_ORYSI_39946 and tr_A0A0E0NPS8_A0A0E0NPS8_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A2XCL6_A2XCL6_ORYSI_39946 and tr_A0A0D3FDX3_A0A0D3FDX3_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A2XCL6_A2XCL6_ORYSI_39946 and tr_A0A0D9Z263_A0A0D9Z263_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A2XCL6_A2XCL6_ORYSI_39946 and tr_Q10RP0_Q10RP0_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1Q5Z6_I1Q5Z6_ORYGL_4538 and tr_A0A0E0M837_A0A0E0M837_ORYPU_4537 are exactly identical!
WARNING: Sequences tr_G2XQL1_G2XQL1_BOTF4_999810 and tr_M7URB7_M7URB7_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_A0A078FLX9_A0A078FLX9_BRANA_3708 and tr_A0A0D3CTJ9_A0A0D3CTJ9_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0F8XC00_A0A0F8XC00_9EURO_308745 and tr_A0A2T5LLJ2_A0A2T5LLJ2_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A1S3WXP8_A0A1S3WXP8_TOBAC_4097 and tr_A0A1U7X6D0_A0A1U7X6D0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3UTH2_A0A1S3UTH2_VIGRR_3916 and tr_A0A3Q0F891_A0A3Q0F891_VIGRR_3916 are exactly identical!
WARNING: Duplicate sequences found: 28

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/O43933/4_raxmlng_ancestral/O43933.raxml.reduced.phy

Alignment comprises 1 partitions and 1283 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 1283
Gaps: 30.17 %
Invariant sites: 0.70 %


NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43933/4_raxmlng_ancestral/O43933.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/O43933/3_mltree/O43933.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 321 / 25680
[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: -591628.915653

[00:00:00 -591628.915653] Initial branch length optimization
[00:00:03 -588423.587601] Model parameter optimization (eps = 0.100000)

[00:01:01] Tree #1, final logLikelihood: -587752.444831


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.116573,0.213674) (0.170843,0.350839) (0.316954,0.751495) (0.395629,1.711105) 
   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/O43933/4_raxmlng_ancestral/O43933.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43933/4_raxmlng_ancestral/O43933.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43933/4_raxmlng_ancestral/O43933.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43933/4_raxmlng_ancestral/O43933.raxml.log

Analysis started: 02-Jun-2021 22:50:16 / finished: 02-Jun-2021 22:51:29

Elapsed time: 72.919 seconds