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 22:49:31 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8N119/2_msa/Q8N119_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8N119/3_mltree/Q8N119.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8N119/4_raxmlng_ancestral/Q8N119 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622663371
  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/Q8N119/2_msa/Q8N119_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 569 sites

WARNING: Sequences tr_G3S700_G3S700_GORGO_9595 and tr_H2QB81_H2QB81_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S700_G3S700_GORGO_9595 and sp_P51511_MMP15_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PXU2_H2PXU2_PANTR_9598 and sp_O75900_MMP23_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A0E0HLF1_A0A0E0HLF1_ORYNI_4536 and tr_A2X9G3_A2X9G3_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0HLF1_A0A0E0HLF1_ORYNI_4536 and tr_Q6Z7S6_Q6Z7S6_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0IWD9_A0A0E0IWD9_ORYNI_4536 and tr_A2ZA53_A2ZA53_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0IWD9_A0A0E0IWD9_ORYNI_4536 and tr_A0A0E0R2D8_A0A0E0R2D8_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0IWD9_A0A0E0IWD9_ORYNI_4536 and tr_A0A0D3HGI7_A0A0D3HGI7_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_F7F147_F7F147_MACMU_9544 and tr_A0A096NIY8_A0A096NIY8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7F147_F7F147_MACMU_9544 and tr_A0A2K5NGB0_A0A2K5NGB0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7F147_F7F147_MACMU_9544 and tr_A0A2K6CWE1_A0A2K6CWE1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7FE85_F7FE85_MACMU_9544 and tr_G7PNJ9_G7PNJ9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7FE85_F7FE85_MACMU_9544 and tr_A0A096N6P6_A0A096N6P6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7FE85_F7FE85_MACMU_9544 and tr_A0A0D9S1T7_A0A0D9S1T7_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7FE85_F7FE85_MACMU_9544 and tr_A0A2K5P0Y0_A0A2K5P0Y0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7FE85_F7FE85_MACMU_9544 and tr_A0A2K5YEA4_A0A2K5YEA4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A2YB49_A2YB49_ORYSI_39946 and tr_A0A0E0PVL7_A0A0E0PVL7_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A2YB49_A2YB49_ORYSI_39946 and tr_Q67VB1_Q67VB1_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A2ZA56_A2ZA56_ORYSI_39946 and tr_Q94LQ0_Q94LQ0_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1P448_I1P448_ORYGL_4538 and tr_A0A0D3FAB1_A0A0D3FAB1_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1QVV8_I1QVV8_ORYGL_4538 and tr_Q94LQ4_Q94LQ4_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A096MQT1_A0A096MQT1_PAPAN_9555 and tr_A0A2K6BUC2_A0A2K6BUC2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A078FNH3_A0A078FNH3_BRANA_3708 and tr_A0A0D3CCW1_A0A0D3CCW1_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_V4TEL9_V4TEL9_9ROSI_85681 and tr_A0A2H5N9J6_A0A2H5N9J6_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A022Q2B7_A0A022Q2B7_ERYGU_4155 and tr_A0A022QM12_A0A022QM12_ERYGU_4155 are exactly identical!
WARNING: Sequences tr_A0A0V0V3V3_A0A0V0V3V3_9BILA_181606 and tr_A0A0V0ZRG6_A0A0V0ZRG6_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0V3V3_A0A0V0V3V3_9BILA_181606 and tr_A0A0V1NTX0_A0A0V1NTX0_9BILA_92180 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/Q8N119/4_raxmlng_ancestral/Q8N119.raxml.reduced.phy

Alignment comprises 1 partitions and 569 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 569
Gaps: 49.08 %
Invariant sites: 0.00 %


NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8N119/4_raxmlng_ancestral/Q8N119.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/Q8N119/3_mltree/Q8N119.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 143 / 11440
[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: -227433.447951

[00:00:00 -227433.447951] Initial branch length optimization
[00:00:01 -226429.601876] Model parameter optimization (eps = 0.100000)

[00:00:48] Tree #1, final logLikelihood: -225771.608814


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.088035,0.285875) (0.103233,0.324482) (0.387991,0.772719) (0.420741,1.524756) 
   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/Q8N119/4_raxmlng_ancestral/Q8N119.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8N119/4_raxmlng_ancestral/Q8N119.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8N119/4_raxmlng_ancestral/Q8N119.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8N119/4_raxmlng_ancestral/Q8N119.raxml.log

Analysis started: 02-Jun-2021 22:49:31 / finished: 02-Jun-2021 22:50:24

Elapsed time: 53.597 seconds