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 03-Jun-2021 01:53:53 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22413/2_msa/P22413_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22413/3_mltree/P22413.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22413/4_raxmlng_ancestral/P22413 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622674433
  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/P22413/2_msa/P22413_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 925 sites

WARNING: Sequences tr_A0A0D8JUS3_A0A0D8JUS3_COCIM_246410 and tr_A0A0J6YQB5_A0A0J6YQB5_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B2WCX1_B2WCX1_PYRTR_426418 and tr_A0A317BKB7_A0A317BKB7_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_B8NFZ8_B8NFZ8_ASPFN_332952 and tr_Q2UE12_Q2UE12_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NFZ8_B8NFZ8_ASPFN_332952 and tr_A0A1S9E001_A0A1S9E001_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_F9FZD1_F9FZD1_FUSOF_660025 and tr_X0D4V1_X0D4V1_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FZD1_F9FZD1_FUSOF_660025 and tr_A0A2H3TDZ7_A0A2H3TDZ7_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A0A0E0FHM7_A0A0E0FHM7_ORYNI_4536 and tr_A0A0E0MSM3_A0A0E0MSM3_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0FHM7_A0A0E0FHM7_ORYNI_4536 and tr_Q7F5L2_Q7F5L2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F7CJD6_F7CJD6_MACMU_9544 and tr_A0A2K5NMP3_A0A2K5NMP3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7GTS7_F7GTS7_MACMU_9544 and tr_A0A2K6BFQ7_A0A2K6BFQ7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7XTP9_G7XTP9_ASPKW_1033177 and tr_A0A146G100_A0A146G100_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G2XNS3_G2XNS3_BOTF4_999810 and tr_M7TPW5_M7TPW5_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_G7P4R8_G7P4R8_MACFA_9541 and tr_A0A2K6BE32_A0A2K6BE32_MACNE_9545 are exactly identical!
WARNING: Sequences tr_M4E5T4_M4E5T4_BRARP_51351 and tr_A0A078GY87_A0A078GY87_BRANA_3708 are exactly identical!
WARNING: Sequences tr_A0A015K6Y5_A0A015K6Y5_9GLOM_1432141 and tr_A0A2H5RLU1_A0A2H5RLU1_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A096NDW2_A0A096NDW2_PAPAN_9555 and tr_A0A2K6BVV8_A0A2K6BVV8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NIR3_A0A096NIR3_PAPAN_9555 and tr_A0A2K5NVR8_A0A2K5NVR8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NIR3_A0A096NIR3_PAPAN_9555 and tr_A0A2K5Z3G6_A0A2K5Z3G6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_V4TVV7_V4TVV7_9ROSI_85681 and tr_A0A2H5PUX6_A0A2H5PUX6_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0F8WMS1_A0A0F8WMS1_9EURO_308745 and tr_A0A2T5LUT1_A0A2T5LUT1_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A1S4CJ88_A0A1S4CJ88_TOBAC_4097 and tr_A0A1U7X746_A0A1U7X746_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4CJ89_A0A1S4CJ89_TOBAC_4097 and tr_A0A1U7XGC4_A0A1U7XGC4_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2K5NN41_A0A2K5NN41_CERAT_9531 and tr_A0A2K5XR78_A0A2K5XR78_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 23

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/P22413/4_raxmlng_ancestral/P22413.raxml.reduced.phy

Alignment comprises 1 partitions and 925 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 925
Gaps: 39.23 %
Invariant sites: 0.43 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22413/4_raxmlng_ancestral/P22413.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/P22413/3_mltree/P22413.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 232 / 18560
[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: -313919.504398

[00:00:00 -313919.504398] Initial branch length optimization
[00:00:02 -311744.445742] Model parameter optimization (eps = 0.100000)

[00:01:08] Tree #1, final logLikelihood: -310965.338870


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.127399,0.385367) (0.133912,0.329103) (0.340365,0.769311) (0.398324,1.619254) 
   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/P22413/4_raxmlng_ancestral/P22413.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22413/4_raxmlng_ancestral/P22413.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22413/4_raxmlng_ancestral/P22413.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P22413/4_raxmlng_ancestral/P22413.raxml.log

Analysis started: 03-Jun-2021 01:53:53 / finished: 03-Jun-2021 01:55:11

Elapsed time: 77.164 seconds

Consumed energy: 6.148 Wh