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 12-Jul-2021 17:43:29 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NVY1/2_msa/Q6NVY1_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NVY1/3_mltree/Q6NVY1.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NVY1/4_raxmlng_ancestral/Q6NVY1 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626101009
  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/300621_run/phylogeny-snakemake/results/Q6NVY1/2_msa/Q6NVY1_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 386 sites

WARNING: Sequences tr_B2W7S4_B2W7S4_PYRTR_426418 and tr_A0A2W1CZQ3_A0A2W1CZQ3_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_A0A0R3NKE4_A0A0R3NKE4_DROPS_46245 and tr_B4GNT9_B4GNT9_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A179V0L7_A0A179V0L7_BLAGS_559298 and tr_C5GL55_C5GL55_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9FMN0_F9FMN0_FUSOF_660025 and tr_N4U7C3_N4U7C3_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FMN0_F9FMN0_FUSOF_660025 and tr_A0A2H3T511_A0A2H3T511_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_C6HKL7_C6HKL7_AJECH_544712 and tr_F0UH88_F0UH88_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_J4USB2_J4USB2_BEAB2_655819 and tr_A0A0A2VRH6_A0A0A2VRH6_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_G7XWX1_G7XWX1_ASPKW_1033177 and tr_A0A100IKW0_A0A100IKW0_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XWX1_G7XWX1_ASPKW_1033177 and tr_A0A146EYP5_A0A146EYP5_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A0A0D2XD13_A0A0D2XD13_FUSO4_426428 and tr_X0DA01_X0DA01_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F2Q0E8_F2Q0E8_TRIEC_559882 and tr_A0A059JK59_A0A059JK59_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_M4ESM2_M4ESM2_BRARP_51351 and tr_A0A078IXV9_A0A078IXV9_BRANA_3708 are exactly identical!
WARNING: Sequences tr_V2X4T1_V2X4T1_MONRO_1381753 and tr_A0A0W0FPT0_A0A0W0FPT0_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2PXY5_W2PXY5_PHYPN_761204 and tr_W2GE15_W2GE15_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015L329_A0A015L329_9GLOM_1432141 and tr_A0A2H5SYL1_A0A2H5SYL1_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A044V4H1_A0A044V4H1_ONCVO_6282 and tr_A0A182E288_A0A182E288_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A0D3EU23_A0A0D3EU23_9ORYZ_65489 and tr_Q5JMX9_Q5JMX9_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_V4U3E1_V4U3E1_9ROSI_85681 and tr_A0A2H5NNX9_A0A2H5NNX9_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0A1NFY4_A0A0A1NFY4_9FUNG_58291 and tr_A0A367KH94_A0A367KH94_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A164QUU8_A0A164QUU8_9HOMO_1314777 and tr_A0A166E549_A0A166E549_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S4BWK8_A0A1S4BWK8_TOBAC_4097 and tr_A0A1U7XTU8_A0A1U7XTU8_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4BWL3_A0A1S4BWL3_TOBAC_4097 and tr_A0A1U7XXP1_A0A1U7XXP1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4C3B5_A0A1S4C3B5_TOBAC_4097 and tr_A0A1U7VQI6_A0A1U7VQI6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1L9NJ92_A0A1L9NJ92_ASPTU_767770 and tr_A0A317UXZ1_A0A317UXZ1_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A0A2K5MI99_A0A2K5MI99_CERAT_9531 and tr_A0A2K5Y7I4_A0A2K5Y7I4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2N5T006_A0A2N5T006_9BASI_200324 and tr_A0A2N5W8G9_A0A2N5W8G9_9BASI_200324 are exactly identical!
WARNING: Duplicate sequences found: 26

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NVY1/4_raxmlng_ancestral/Q6NVY1.raxml.reduced.phy

Alignment comprises 1 partitions and 386 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 386
Gaps: 9.92 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NVY1/4_raxmlng_ancestral/Q6NVY1.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/300621_run/phylogeny-snakemake/results/Q6NVY1/3_mltree/Q6NVY1.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 97 / 7760
[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: -203279.278275

[00:00:00 -203279.278275] Initial branch length optimization
[00:00:01 -202744.348999] Model parameter optimization (eps = 0.100000)

[00:00:25] Tree #1, final logLikelihood: -202413.483825


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.138006,0.247565) (0.240866,0.368221) (0.300467,0.881863) (0.320662,1.909091) 
   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/300621_run/phylogeny-snakemake/results/Q6NVY1/4_raxmlng_ancestral/Q6NVY1.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NVY1/4_raxmlng_ancestral/Q6NVY1.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NVY1/4_raxmlng_ancestral/Q6NVY1.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NVY1/4_raxmlng_ancestral/Q6NVY1.raxml.log

Analysis started: 12-Jul-2021 17:43:29 / finished: 12-Jul-2021 17:43:58

Elapsed time: 29.558 seconds

Consumed energy: 2.449 Wh