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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 02-Jun-2021 18:32:08 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00192/2_msa/O00192_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00192/3_mltree/O00192.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00192/4_raxmlng_ancestral/O00192 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622647928
  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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00192/2_msa/O00192_nogap_msa.fasta
[00:00:00] Loaded alignment with 1000 taxa and 962 sites

WARNING: Sequences tr_A0A2I2ZRH7_A0A2I2ZRH7_GORGO_9595 and sp_Q99569_PKP4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2ZRH7_A0A2I2ZRH7_GORGO_9595 and tr_A0A2R9BFT5_A0A2R9BFT5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2NDF0_H2NDF0_PONAB_9601 and tr_A0A2K6A8L4_A0A2K6A8L4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3RS45_A0A2I3RS45_PANTR_9598 and sp_Q9UQB3_CTND2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2J8KHS3_A0A2J8KHS3_PANTR_9598 and sp_Q13835_PKP1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2J8KHS3_A0A2J8KHS3_PANTR_9598 and tr_A0A2R8ZKP2_A0A2R8ZKP2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0E0HE46_A0A0E0HE46_ORYNI_4536 and tr_A0A0E0PM67_A0A0E0PM67_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_F6ZE57_F6ZE57_MACMU_9544 and tr_G7NWF8_G7NWF8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6ZE57_F6ZE57_MACMU_9544 and tr_A0A0D9RN26_A0A0D9RN26_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6ZE57_F6ZE57_MACMU_9544 and tr_A0A2K6CY12_A0A2K6CY12_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6ZE57_F6ZE57_MACMU_9544 and tr_A0A2K5ZNT1_A0A2K5ZNT1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1M7W0_G1M7W0_AILME_9646 and tr_A0A2U3XBA6_A0A2U3XBA6_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A067FMW6_A0A067FMW6_CITSI_2711 and tr_V4TAH7_V4TAH7_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A2I3N206_A0A2I3N206_PAPAN_9555 and tr_A0A2K5NBB6_A0A2K5NBB6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A078FHR3_A0A078FHR3_BRANA_3708 and tr_A0A0D3EE29_A0A0D3EE29_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A151NXJ0_A0A151NXJ0_ALLMI_8496 and tr_A0A1U7RUG2_A0A1U7RUG2_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091FKE9_A0A091FKE9_CORBR_85066 and tr_A0A091J2G7_A0A091J2G7_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_A0A091FKE9_A0A091FKE9_CORBR_85066 and tr_A0A087QXL3_A0A087QXL3_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091FKE9_A0A091FKE9_CORBR_85066 and tr_A0A0A0ADL3_A0A0A0ADL3_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0V1DFP6_A0A0V1DFP6_TRIBR_45882 and tr_A0A0V1PGV6_A0A0V1PGV6_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A1S3YJL8_A0A1S3YJL8_TOBAC_4097 and tr_A0A1U7XCV9_A0A1U7XCV9_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3J0U1_A0A1S3J0U1_LINUN_7574 and tr_A0A1S3J218_A0A1S3J218_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A226NC43_A0A226NC43_CALSU_9009 and tr_A0A226P375_A0A226P375_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0RCX3_A0A2D0RCX3_ICTPU_7998 and tr_A0A2D0RCX4_A0A2D0RCX4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RCX3_A0A2D0RCX3_ICTPU_7998 and tr_A0A2D0RE31_A0A2D0RE31_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 25

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00192/4_raxmlng_ancestral/O00192.raxml.reduced.phy

Alignment comprises 1 partitions and 962 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 962
Gaps: 34.75 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00192/4_raxmlng_ancestral/O00192.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00192/3_mltree/O00192.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 241 / 19280
[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: -275613.313733

[00:00:00 -275613.313733] Initial branch length optimization
[00:00:02 -245663.831616] Model parameter optimization (eps = 0.100000)

[00:01:09] Tree #1, final logLikelihood: -244555.850259


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.160985,0.424998) (0.078448,0.353259) (0.313684,0.708114) (0.446883,1.525556) 
   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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00192/4_raxmlng_ancestral/O00192.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00192/4_raxmlng_ancestral/O00192.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00192/4_raxmlng_ancestral/O00192.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00192/4_raxmlng_ancestral/O00192.raxml.log

Analysis started: 02-Jun-2021 18:32:08 / finished: 02-Jun-2021 18:33:27

Elapsed time: 79.275 seconds

Consumed energy: 4.771 Wh