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 17:20:39 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/2_msa/Q8N7U6_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/3_mltree/Q8N7U6.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/4_raxmlng_ancestral/Q8N7U6 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626099639
  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/Q8N7U6/2_msa/Q8N7U6_nogap_msa.fasta
[00:00:00] Loaded alignment with 650 taxa and 833 sites

WARNING: Sequences tr_B4QQ02_B4QQ02_DROSI_7240 and sp_P48593_E631_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4QQ02_B4QQ02_DROSI_7240 and tr_B4HTW1_B4HTW1_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B4QQ02_B4QQ02_DROSI_7240 and tr_A0A1W4VQ76_A0A1W4VQ76_DROFC_30025 are exactly identical!
WARNING: Sequences tr_A0A0E0GBF1_A0A0E0GBF1_ORYNI_4536 and tr_A0A0D9YWK4_A0A0D9YWK4_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP0_A0A0E0GUP0_ORYNI_4536 and tr_A2XMQ5_A2XMQ5_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP0_A0A0E0GUP0_ORYNI_4536 and tr_A0A0E0P2A3_A0A0E0P2A3_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP0_A0A0E0GUP0_ORYNI_4536 and sp_Q6F3A6_CDPKA_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP4_A0A0E0GUP4_ORYNI_4536 and tr_A0A0E0P2A9_A0A0E0P2A9_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0H559_A0A0E0H559_ORYNI_4536 and tr_A0A0E0PD86_A0A0E0PD86_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0HWX4_A0A0E0HWX4_ORYNI_4536 and tr_A0A0D3GMK1_A0A0D3GMK1_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A2YIE4_A2YIE4_ORYSI_39946 and sp_Q7XIM0_CDPKH_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_B8ALC3_B8ALC3_ORYSI_39946 and sp_Q852N6_CDPKB_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_B8ATC8_B8ATC8_ORYSI_39946 and sp_Q9FXQ3_CDPKD_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1PG77_I1PG77_ORYGL_4538 and tr_A0A0E0D7Y8_A0A0E0D7Y8_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_I1QER5_I1QER5_ORYGL_4538 and tr_A0A0D3FPZ4_A0A0D3FPZ4_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1R6F0_I1R6F0_ORYGL_4538 and tr_A0A0E0RHE1_A0A0E0RHE1_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1R6F0_I1R6F0_ORYGL_4538 and sp_Q2QQR2_CDPKR_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0NJC7_A0A0E0NJC7_ORYRU_4529 and sp_Q0DYK7_CDPK5_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_B3SDH5_B3SDH5_TRIAD_10228 and tr_A0A369RWC0_A0A369RWC0_9METZ_287889 are exactly identical!
WARNING: Sequences tr_A0A0D2YC47_A0A0D2YC47_FUSO4_426428 and tr_A0A2H3GE91_A0A2H3GE91_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A0D3FPZ7_A0A0D3FPZ7_9ORYZ_65489 and tr_A0A0D9ZE64_A0A0D9ZE64_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A067FQG3_A0A067FQG3_CITSI_2711 and tr_V4RMX8_V4RMX8_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067FTI8_A0A067FTI8_CITSI_2711 and tr_A0A2H5MXZ8_A0A2H5MXZ8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A078F7M3_A0A078F7M3_BRANA_3708 and tr_A0A078FNE3_A0A078FNE3_BRANA_3708 are exactly identical!
WARNING: Sequences tr_A0A0D2PM25_A0A0D2PM25_GOSRA_29730 and tr_A0A1U8LNS6_A0A1U8LNS6_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A1S3XWQ8_A0A1S3XWQ8_TOBAC_4097 and tr_A0A1U7X7I7_A0A1U7X7I7_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4ASR5_A0A1S4ASR5_TOBAC_4097 and tr_A0A1U7X617_A0A1U7X617_NICSY_4096 are exactly identical!
WARNING: Sequences tr_Q93YF3_Q93YF3_TOBAC_4097 and tr_A0A1U7UTS3_A0A1U7UTS3_NICSY_4096 are exactly identical!
WARNING: Sequences tr_Q93YF4_Q93YF4_TOBAC_4097 and tr_A0A1U7VH25_A0A1U7VH25_NICSY_4096 are exactly identical!
WARNING: Duplicate sequences found: 29

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/Q8N7U6/4_raxmlng_ancestral/Q8N7U6.raxml.reduced.phy

Alignment comprises 1 partitions and 833 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 833
Gaps: 51.39 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/4_raxmlng_ancestral/Q8N7U6.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/Q8N7U6/3_mltree/Q8N7U6.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 209 / 16720
[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: -149206.181819

[00:00:00 -149206.181819] Initial branch length optimization
[00:00:01 -146158.188366] Model parameter optimization (eps = 0.100000)

[00:00:41] Tree #1, final logLikelihood: -145111.722629


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.147879,0.358348) (0.095410,0.427497) (0.413144,0.605934) (0.343567,1.909037) 
   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/Q8N7U6/4_raxmlng_ancestral/Q8N7U6.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/4_raxmlng_ancestral/Q8N7U6.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/4_raxmlng_ancestral/Q8N7U6.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/4_raxmlng_ancestral/Q8N7U6.raxml.log

Analysis started: 12-Jul-2021 17:20:39 / finished: 12-Jul-2021 17:21:25

Elapsed time: 45.802 seconds

Consumed energy: 3.105 Wh