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 22:43:55 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54886/2_msa/P54886_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54886/3_mltree/P54886.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54886/4_raxmlng_ancestral/P54886 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622663035
  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/P54886/2_msa/P54886_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 795 sites

WARNING: Sequences tr_B6Q8S3_B6Q8S3_TALMQ_441960 and tr_A0A093VLL9_A0A093VLL9_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WMZ2_B2WMZ2_PYRTR_426418 and tr_A0A2W1E8P2_A0A2W1E8P2_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_K7D0Y1_K7D0Y1_PANTR_9598 and sp_P54886_P5CS_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_K7D0Y1_K7D0Y1_PANTR_9598 and tr_A0A2R9C489_A0A2R9C489_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FUI9_F9FUI9_FUSOF_660025 and tr_X0CJ04_X0CJ04_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FUI9_F9FUI9_FUSOF_660025 and tr_A0A2H3SMU3_A0A2H3SMU3_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A0A0E0FVQ6_A0A0E0FVQ6_ORYNI_4536 and tr_A0A0E0N4Z1_A0A0E0N4Z1_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0FVQ6_A0A0E0FVQ6_ORYNI_4536 and tr_A0A0D3EW86_A0A0D3EW86_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0FVQ6_A0A0E0FVQ6_ORYNI_4536 and tr_A0A0D9YHA9_A0A0D9YHA9_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_G7N2M0_G7N2M0_MACMU_9544 and tr_G7PDM0_G7PDM0_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7XHB5_G7XHB5_ASPKW_1033177 and tr_A0A124BZ10_A0A124BZ10_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XHB5_G7XHB5_ASPKW_1033177 and tr_A0A1L9MUP2_A0A1L9MUP2_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_B8AC46_B8AC46_ORYSI_39946 and tr_I1NTB9_I1NTB9_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_B8AC46_B8AC46_ORYSI_39946 and sp_Q941T1_P5CS2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_B8AYT8_B8AYT8_ORYSI_39946 and tr_A0A0E0A052_A0A0E0A052_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_F4NZZ4_F4NZZ4_BATDJ_684364 and tr_A0A177WE30_A0A177WE30_BATDE_403673 are exactly identical!
WARNING: Sequences tr_G2YAB4_G2YAB4_BOTF4_999810 and tr_M7UDA5_M7UDA5_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SNY6_F2SNY6_TRIRC_559305 and tr_A0A178F4A6_A0A178F4A6_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_G3XV29_G3XV29_ASPNA_380704 and tr_A0A319ALQ1_A0A319ALQ1_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A0A0D2XMV7_A0A0D2XMV7_FUSO4_426428 and tr_A0A2H3GZD7_A0A2H3GZD7_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_M4BHJ5_M4BHJ5_HYAAE_559515 and tr_M4BHK1_M4BHK1_HYAAE_559515 are exactly identical!
WARNING: Sequences tr_M7YJV0_M7YJV0_TRIUA_4572 and tr_A0A3B6ENH3_A0A3B6ENH3_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_V2XF05_V2XF05_MONRO_1381753 and tr_A0A0W0FXP7_A0A0W0FXP7_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2QYM4_W2QYM4_PHYPN_761204 and tr_W2G0X7_W2G0X7_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015I3C8_A0A015I3C8_9GLOM_1432141 and tr_A0A2H5SR70_A0A2H5SR70_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A078JDW4_A0A078JDW4_BRANA_3708 and tr_A0A0D3BXP3_A0A0D3BXP3_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A094E899_A0A094E899_9PEZI_1420912 and tr_A0A1B8GMY9_A0A1B8GMY9_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0F8WRI2_A0A0F8WRI2_9EURO_308745 and tr_A0A2T5LQV3_A0A2T5LQV3_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A1R3RCS1_A0A1R3RCS1_ASPC5_602072 and tr_A0A1R3RCZ9_A0A1R3RCZ9_ASPC5_602072 are exactly identical!
WARNING: Sequences tr_A0A1Q3EFJ7_A0A1Q3EFJ7_LENED_5353 and tr_A0A1Q3EFL3_A0A1Q3EFL3_LENED_5353 are exactly identical!
WARNING: Sequences tr_A0A2G2Z8V8_A0A2G2Z8V8_CAPAN_4072 and tr_A0A2G3C5D9_A0A2G3C5D9_CAPCH_80379 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/P54886/4_raxmlng_ancestral/P54886.raxml.reduced.phy

Alignment comprises 1 partitions and 795 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 795
Gaps: 31.51 %
Invariant sites: 0.13 %


NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54886/4_raxmlng_ancestral/P54886.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/P54886/3_mltree/P54886.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 199 / 15920
[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: -245896.160140

[00:00:00 -245896.160140] Initial branch length optimization
[00:00:01 -243817.114406] Model parameter optimization (eps = 0.100000)

[00:00:36] Tree #1, final logLikelihood: -243290.312695


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.240978,0.260359) (0.262910,0.410943) (0.247263,0.961512) (0.248850,2.376827) 
   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/P54886/4_raxmlng_ancestral/P54886.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54886/4_raxmlng_ancestral/P54886.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54886/4_raxmlng_ancestral/P54886.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54886/4_raxmlng_ancestral/P54886.raxml.log

Analysis started: 02-Jun-2021 22:43:55 / finished: 02-Jun-2021 22:44:38

Elapsed time: 43.147 seconds