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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 02-Jun-2021 17:55:34 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99497/2_msa/Q99497_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99497/3_mltree/Q99497.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99497/4_raxmlng_ancestral/Q99497 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622645734
  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/Q99497/2_msa/Q99497_nogap_msa.fasta
[00:00:00] Loaded alignment with 798 taxa and 189 sites

WARNING: Sequences tr_D5M8S2_D5M8S2_CHICK_9031 and tr_G1MQE7_G1MQE7_MELGA_9103 are exactly identical!
WARNING: Sequences tr_A0A2I3HIU7_A0A2I3HIU7_NOMLE_61853 and sp_Q99497_PARK7_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3HIU7_A0A2I3HIU7_NOMLE_61853 and tr_A0A2I3M4I5_A0A2I3M4I5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3HIU7_A0A2I3HIU7_NOMLE_61853 and tr_A0A2K6BKD2_A0A2K6BKD2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3HIU7_A0A2I3HIU7_NOMLE_61853 and tr_A0A2K5YG64_A0A2K5YG64_MANLE_9568 are exactly identical!
WARNING: Sequences tr_B2W605_B2W605_PYRTR_426418 and tr_A0A2W1G4C4_A0A2W1G4C4_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_Q29CB8_Q29CB8_DROPS_46245 and tr_B4GNB4_B4GNB4_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A2I3SNT8_A0A2I3SNT8_PANTR_9598 and tr_A0A0D9S8R1_A0A0D9S8R1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3SNT8_A0A2I3SNT8_PANTR_9598 and tr_A0A2R9AGT7_A0A2R9AGT7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A158P367_A0A158P367_ATTCE_12957 and tr_A0A195BHE3_A0A195BHE3_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A0E0FIH9_A0A0E0FIH9_ORYNI_4536 and tr_B8AAK7_B8AAK7_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0FIH9_A0A0E0FIH9_ORYNI_4536 and tr_I1NLA9_I1NLA9_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0FIH9_A0A0E0FIH9_ORYNI_4536 and tr_A0A0E0MT46_A0A0E0MT46_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0FIH9_A0A0E0FIH9_ORYNI_4536 and tr_A0A0D9Y581_A0A0D9Y581_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0FIH9_A0A0E0FIH9_ORYNI_4536 and tr_Q0JPK7_Q0JPK7_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F4P7U3_F4P7U3_BATDJ_684364 and tr_A0A177WUA0_A0A177WUA0_BATDE_403673 are exactly identical!
WARNING: Sequences tr_I1Q2R6_I1Q2R6_ORYGL_4538 and tr_Q5Z790_Q5Z790_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_B5G3Z6_B5G3Z6_TAEGU_59729 and tr_A0A218ULT8_A0A218ULT8_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A0E0MT42_A0A0E0MT42_ORYRU_4529 and tr_Q5QNF2_Q5QNF2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0PYQ0_A0A0E0PYQ0_ORYRU_4529 and tr_A0A0D3GHE9_A0A0D3GHE9_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0PYQ0_A0A0E0PYQ0_ORYRU_4529 and tr_A0A0E0AAG4_A0A0E0AAG4_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_D2HA21_D2HA21_AILME_9646 and tr_A0A2U3VQX2_A0A2U3VQX2_ODORO_9708 are exactly identical!
WARNING: Sequences tr_W2PTS1_W2PTS1_PHYPN_761204 and tr_W2GAD4_W2GAD4_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A3B6I0B1_A0A3B6I0B1_WHEAT_4565 and tr_A0A3B6R8F5_A0A3B6R8F5_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A158N7S9_A0A158N7S9_ONCVO_6282 and tr_A0A182DZN9_A0A182DZN9_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A067F977_A0A067F977_CITSI_2711 and tr_V4S745_V4S745_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A091VVM2_A0A091VVM2_NIPNI_128390 and tr_A0A091W791_A0A091W791_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A0V1KXS2_A0A0V1KXS2_9BILA_6335 and tr_A0A0V0U3J7_A0A0V0U3J7_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S4A7E9_A0A1S4A7E9_TOBAC_4097 and tr_A0A1U7VC80_A0A1U7VC80_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2G2Z591_A0A2G2Z591_CAPAN_4072 and tr_B1Q484_B1Q484_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2I1GG62_A0A2I1GG62_9GLOM_588596 and tr_U9UYK3_U9UYK3_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2H5QPB7_A0A2H5QPB7_CITUN_55188 and tr_A0A2H5QPE6_A0A2H5QPE6_CITUN_55188 are exactly identical!
WARNING: Duplicate sequences found: 32

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/Q99497/4_raxmlng_ancestral/Q99497.raxml.reduced.phy

Alignment comprises 1 partitions and 189 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 189
Gaps: 9.03 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99497/4_raxmlng_ancestral/Q99497.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/Q99497/3_mltree/Q99497.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 48 / 3840
[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: -87363.985164

[00:00:00 -87363.985164] Initial branch length optimization
[00:00:00 -87210.716160] Model parameter optimization (eps = 0.100000)

[00:00:16] Tree #1, final logLikelihood: -86786.726408


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.165744,0.438813) (0.260615,0.434109) (0.289473,0.838346) (0.284168,2.010977) 
   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/Q99497/4_raxmlng_ancestral/Q99497.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99497/4_raxmlng_ancestral/Q99497.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99497/4_raxmlng_ancestral/Q99497.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99497/4_raxmlng_ancestral/Q99497.raxml.log

Analysis started: 02-Jun-2021 17:55:34 / finished: 02-Jun-2021 17:55:52

Elapsed time: 17.368 seconds

Consumed energy: 1.536 Wh