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 03-Jun-2021 02:04:48 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49748/2_msa/P49748_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49748/3_mltree/P49748.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49748/4_raxmlng_ancestral/P49748 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622675088
  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/P49748/2_msa/P49748_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 655 sites

WARNING: Sequences tr_J3KAZ8_J3KAZ8_COCIM_246410 and tr_A0A0J6YK26_A0A0J6YK26_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QAV8_B6QAV8_TALMQ_441960 and tr_A0A093VF69_A0A093VF69_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_G3QI49_G3QI49_GORGO_9595 and sp_Q5RAS0_ACADS_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QI49_G3QI49_GORGO_9595 and tr_H2Q719_H2Q719_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QI49_G3QI49_GORGO_9595 and tr_A0A0D9S4L4_A0A0D9S4L4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3QI49_G3QI49_GORGO_9595 and tr_A0A2R8ZI63_A0A2R8ZI63_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q294T1_Q294T1_DROPS_46245 and tr_B4GMN1_B4GMN1_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q2M0E5_Q2M0E5_DROPS_46245 and tr_B4GRR0_B4GRR0_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B8MZJ2_B8MZJ2_ASPFN_332952 and tr_Q2UQH2_Q2UQH2_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8MZJ2_B8MZJ2_ASPFN_332952 and tr_A0A0F0I4V8_A0A0F0I4V8_ASPPU_1403190 are exactly identical!
WARNING: Sequences tr_B8MZJ2_B8MZJ2_ASPFN_332952 and tr_A0A2G7FVA5_A0A2G7FVA5_9EURO_656916 are exactly identical!
WARNING: Sequences tr_H2QNB4_H2QNB4_PANTR_9598 and sp_Q9H845_ACAD9_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F9FME3_F9FME3_FUSOF_660025 and tr_A0A0D2XWP3_A0A0D2XWP3_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FME3_F9FME3_FUSOF_660025 and tr_N4UG87_N4UG87_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FME3_F9FME3_FUSOF_660025 and tr_X0CEF0_X0CEF0_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FME3_F9FME3_FUSOF_660025 and tr_A0A2H3T8U8_A0A2H3T8U8_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FME3_F9FME3_FUSOF_660025 and tr_A0A2H3I217_A0A2H3I217_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_C6HNX7_C6HNX7_AJECH_544712 and tr_F0UGF1_F0UGF1_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A2QAV9_A2QAV9_ASPNC_425011 and tr_G3XRH8_G3XRH8_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_G0N9T5_G0N9T5_CAEBE_135651 and tr_G0PH78_G0PH78_CAEBE_135651 are exactly identical!
WARNING: Sequences tr_G2YM87_G2YM87_BOTF4_999810 and tr_M7TZU0_M7TZU0_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_W2PDK7_W2PDK7_PHYPN_761204 and tr_A0A0W8CQR3_A0A0W8CQR3_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PDK7_W2PDK7_PHYPN_761204 and tr_W2JPZ0_W2JPZ0_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2Q743_W2Q743_PHYPN_761204 and tr_W2J1T5_W2J1T5_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2QTY6_W2QTY6_PHYPN_761204 and tr_A0A0W8C7U1_A0A0W8C7U1_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QTY6_W2QTY6_PHYPN_761204 and tr_W2JQK9_W2JQK9_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A0V1CS61_A0A0V1CS61_TRIBR_45882 and tr_A0A0V0UUU3_A0A0V0UUU3_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CS61_A0A0V1CS61_TRIBR_45882 and tr_A0A0V1KT93_A0A0V1KT93_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1CS61_A0A0V1CS61_TRIBR_45882 and tr_A0A0V1NG55_A0A0V1NG55_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CS61_A0A0V1CS61_TRIBR_45882 and tr_A0A0V0TTK0_A0A0V0TTK0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A164VD59_A0A164VD59_9HOMO_1314777 and tr_A0A165Z246_A0A165Z246_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1B8GWX6_A0A1B8GWX6_9PEZI_342668 and tr_A0A1B8CB31_A0A1B8CB31_9PEZI_1622147 are exactly identical!
WARNING: Sequences tr_A0A1B8GWX6_A0A1B8GWX6_9PEZI_342668 and tr_A0A1B8EVG8_A0A1B8EVG8_9PEZI_1622149 are exactly identical!
WARNING: Duplicate sequences found: 33

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/P49748/4_raxmlng_ancestral/P49748.raxml.reduced.phy

Alignment comprises 1 partitions and 655 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 655
Gaps: 29.46 %
Invariant sites: 0.15 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49748/4_raxmlng_ancestral/P49748.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/P49748/3_mltree/P49748.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 164 / 13120
[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: -235110.654137

[00:00:00 -235110.654137] Initial branch length optimization
[00:00:01 -232691.184183] Model parameter optimization (eps = 0.100000)

[00:00:38] Tree #1, final logLikelihood: -231937.461662


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.193881,0.311852) (0.258272,0.396093) (0.296010,0.960023) (0.251837,2.196111) 
   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/P49748/4_raxmlng_ancestral/P49748.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49748/4_raxmlng_ancestral/P49748.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49748/4_raxmlng_ancestral/P49748.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49748/4_raxmlng_ancestral/P49748.raxml.log

Analysis started: 03-Jun-2021 02:04:48 / finished: 03-Jun-2021 02:05:33

Elapsed time: 44.312 seconds

Consumed energy: 3.053 Wh