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 20-Jul-2021 16:34:36 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96PX6/2_msa/Q96PX6_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96PX6/3_mltree/Q96PX6.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96PX6/4_raxmlng_ancestral/Q96PX6 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626788076
  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/Q96PX6/2_msa/Q96PX6_nogap_msa.fasta
[00:00:00] Loaded alignment with 376 taxa and 553 sites

WARNING: Sequences sp_Q6PDY0_CC85B_MOUSE_10090 and tr_G3I2G2_G3I2G2_CRIGR_10029 are exactly identical!
WARNING: Sequences sp_Q6PDY0_CC85B_MOUSE_10090 and tr_A0A1U7Q2U9_A0A1U7Q2U9_MESAU_10036 are exactly identical!
WARNING: Sequences tr_M3Z8D9_M3Z8D9_MUSPF_9669 and tr_A0A2I3HE63_A0A2I3HE63_NOMLE_61853 are exactly identical!
WARNING: Sequences tr_M3Z8D9_M3Z8D9_MUSPF_9669 and tr_E2REF8_E2REF8_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3Z8D9_M3Z8D9_MUSPF_9669 and tr_H0XLU9_H0XLU9_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_M3Z8D9_M3Z8D9_MUSPF_9669 and tr_A0A337SJP2_A0A337SJP2_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3Z8D9_M3Z8D9_MUSPF_9669 and tr_A0A2U3VGR8_A0A2U3VGR8_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Z8D9_M3Z8D9_MUSPF_9669 and tr_A0A2U3Y925_A0A2U3Y925_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3Z8D9_M3Z8D9_MUSPF_9669 and tr_A0A2Y9JSZ7_A0A2Y9JSZ7_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I2ZME5_A0A2I2ZME5_GORGO_9595 and tr_A0A2I3LY10_A0A2I3LY10_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I2ZME5_A0A2I2ZME5_GORGO_9595 and tr_A0A2K5XHK1_A0A2K5XHK1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2ZME5_A0A2I2ZME5_GORGO_9595 and tr_A0A2R9A2C9_A0A2R9A2C9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2NCT3_H2NCT3_PONAB_9601 and tr_H2Q448_H2Q448_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2NCT3_H2NCT3_PONAB_9601 and sp_Q15834_CC85B_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2NCT3_H2NCT3_PONAB_9601 and tr_F7F848_F7F848_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2NCT3_H2NCT3_PONAB_9601 and tr_A0A096N9K3_A0A096N9K3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2NCT3_H2NCT3_PONAB_9601 and tr_A0A0D9SCU1_A0A0D9SCU1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_K7AAL2_K7AAL2_PANTR_9598 and sp_A6NKD9_CC85C_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A158NYV0_A0A158NYV0_ATTCE_12957 and tr_A0A195BUI1_A0A195BUI1_9HYME_520822 are exactly identical!
WARNING: Sequences tr_I3M200_I3M200_ICTTR_43179 and tr_A0A1S3FIK1_A0A1S3FIK1_DIPOR_10020 are exactly identical!
WARNING: Sequences tr_F1RU25_F1RU25_PIG_9823 and tr_F1N5D5_F1N5D5_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_F1RU25_F1RU25_PIG_9823 and tr_A0A2U3UZL7_A0A2U3UZL7_TURTR_9739 are exactly identical!
WARNING: Sequences tr_F1RU25_F1RU25_PIG_9823 and tr_A0A2Y9PUX1_A0A2Y9PUX1_DELLE_9749 are exactly identical!
WARNING: Sequences tr_F1RU25_F1RU25_PIG_9823 and tr_A0A2Y9FRQ8_A0A2Y9FRQ8_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A0D9RDI2_A0A0D9RDI2_CHLSB_60711 and tr_A0A2K5MZC4_A0A2K5MZC4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A226N9Q9_A0A226N9Q9_CALSU_9009 and tr_A0A226PHV3_A0A226PHV3_COLVI_9014 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/Q96PX6/4_raxmlng_ancestral/Q96PX6.raxml.reduced.phy

Alignment comprises 1 partitions and 553 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 553
Gaps: 45.33 %
Invariant sites: 3.07 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96PX6/4_raxmlng_ancestral/Q96PX6.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/Q96PX6/3_mltree/Q96PX6.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 139 / 11120
[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: -80863.992242

[00:00:00 -80863.992242] Initial branch length optimization
[00:00:00 -62735.537220] Model parameter optimization (eps = 0.100000)

[00:00:31] Tree #1, final logLikelihood: -62202.545897


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.141425,2.201284) (0.064692,0.129344) (0.352091,0.441098) (0.441791,1.188363) 
   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/Q96PX6/4_raxmlng_ancestral/Q96PX6.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96PX6/4_raxmlng_ancestral/Q96PX6.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96PX6/4_raxmlng_ancestral/Q96PX6.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96PX6/4_raxmlng_ancestral/Q96PX6.raxml.log

Analysis started: 20-Jul-2021 16:34:36 / finished: 20-Jul-2021 16:35:09

Elapsed time: 33.014 seconds