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 19-Jul-2021 13:24:57 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96BJ8/2_msa/Q96BJ8_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96BJ8/3_mltree/Q96BJ8.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96BJ8/4_raxmlng_ancestral/Q96BJ8 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626690297
  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_300621/phylogeny-snakemake/results/Q96BJ8/2_msa/Q96BJ8_nogap_msa.fasta
[00:00:00] Loaded alignment with 444 taxa and 720 sites

WARNING: Sequences sp_Q8BPU7_ELMO1_MOUSE_10090 and tr_G8CYZ7_G8CYZ7_RAT_10116 are exactly identical!
WARNING: Sequences tr_G1QQ57_G1QQ57_NOMLE_61853 and sp_Q92556_ELMO1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QQ57_G1QQ57_NOMLE_61853 and tr_F7IAL7_F7IAL7_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3RDW1_G3RDW1_GORGO_9595 and tr_A0A2J8XVA6_A0A2J8XVA6_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RDW1_G3RDW1_GORGO_9595 and tr_H2QKI4_H2QKI4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RDW1_G3RDW1_GORGO_9595 and sp_Q96JJ3_ELMO2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RDW1_G3RDW1_GORGO_9595 and tr_F6WWC5_F6WWC5_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3RDW1_G3RDW1_GORGO_9595 and tr_G7PG35_G7PG35_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3RDW1_G3RDW1_GORGO_9595 and tr_A0A096NLX7_A0A096NLX7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3RDW1_G3RDW1_GORGO_9595 and tr_A0A0D9RQJ4_A0A0D9RQJ4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3RDW1_G3RDW1_GORGO_9595 and tr_A0A2K5L4W5_A0A2K5L4W5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3RDW1_G3RDW1_GORGO_9595 and tr_A0A2K6CCL9_A0A2K6CCL9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3RDW1_G3RDW1_GORGO_9595 and tr_A0A2R9A3F4_A0A2R9A3F4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5P079_W5P079_SHEEP_9940 and tr_F1MQH0_F1MQH0_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_H0X197_H0X197_OTOGA_30611 and tr_A0A2R9CS91_A0A2R9CS91_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7DM33_F7DM33_MACMU_9544 and tr_A0A096N5B1_A0A096N5B1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7DM33_F7DM33_MACMU_9544 and tr_A0A0D9RRB5_A0A0D9RRB5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7DM33_F7DM33_MACMU_9544 and tr_A0A2K6ARS9_A0A2K6ARS9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7DM33_F7DM33_MACMU_9544 and tr_A0A2K5YZU2_A0A2K5YZU2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0Z5B2_H0Z5B2_TAEGU_59729 and tr_A0A218V0P2_A0A218V0P2_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A091J4I7_A0A091J4I7_EGRGA_188379 and tr_A0A087QQU5_A0A087QQU5_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A2I0LZI5_A0A2I0LZI5_COLLI_8932 and tr_A0A1V4J5A2_A0A1V4J5A2_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1M5E3_A0A0V1M5E3_9BILA_268474 and tr_A0A0V1GYF6_A0A0V1GYF6_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A1S3Q1Y2_A0A1S3Q1Y2_SALSA_8030 and tr_B5X1Y9_B5X1Y9_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1V4KKU3_A0A1V4KKU3_PATFA_372326 and tr_A0A218UF07_A0A218UF07_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A2U4C2A6_A0A2U4C2A6_TURTR_9739 and tr_A0A2Y9MNV8_A0A2Y9MNV8_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 26

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96BJ8/4_raxmlng_ancestral/Q96BJ8.raxml.reduced.phy

Alignment comprises 1 partitions and 720 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 720
Gaps: 15.70 %
Invariant sites: 0.14 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96BJ8/4_raxmlng_ancestral/Q96BJ8.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_300621/phylogeny-snakemake/results/Q96BJ8/3_mltree/Q96BJ8.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 180 / 14400
[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: -90239.617430

[00:00:00 -90239.617430] Initial branch length optimization
[00:00:00 -90187.843384] Model parameter optimization (eps = 0.100000)

[00:00:28] Tree #1, final logLikelihood: -89702.343383


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.236986,0.474170) (0.162487,0.563829) (0.390408,0.907351) (0.210118,2.102509) 
   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_300621/phylogeny-snakemake/results/Q96BJ8/4_raxmlng_ancestral/Q96BJ8.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96BJ8/4_raxmlng_ancestral/Q96BJ8.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96BJ8/4_raxmlng_ancestral/Q96BJ8.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96BJ8/4_raxmlng_ancestral/Q96BJ8.raxml.log

Analysis started: 19-Jul-2021 13:24:57 / finished: 19-Jul-2021 13:25:28

Elapsed time: 30.934 seconds