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 02:44:23 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06132/2_msa/P06132_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06132/3_mltree/P06132.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06132/4_raxmlng_ancestral/P06132 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622677463
  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/P06132/2_msa/P06132_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 367 sites

WARNING: Sequences tr_B4QHA7_B4QHA7_DROSI_7240 and tr_B4HT11_B4HT11_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A0E1RXF3_A0A0E1RXF3_COCIM_246410 and tr_A0A0J6YBF4_A0A0J6YBF4_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B2WCU5_B2WCU5_PYRTR_426418 and tr_A0A2W1GS24_A0A2W1GS24_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_A0A2I2YAA0_A0A2I2YAA0_GORGO_9595 and tr_H2PYW8_H2PYW8_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YAA0_A0A2I2YAA0_GORGO_9595 and tr_A0A2R9BB53_A0A2R9BB53_PANPA_9597 are exactly identical!
WARNING: Sequences tr_B8N1F1_B8N1F1_ASPFN_332952 and tr_A0A1S9DM70_A0A1S9DM70_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179V0S6_A0A179V0S6_BLAGS_559298 and tr_C5GCV3_C5GCV3_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_A0A0E0GB16_A0A0E0GB16_ORYNI_4536 and tr_B8ABY1_B8ABY1_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A2Q8G4_A2Q8G4_ASPNC_425011 and tr_G3XRX3_G3XRX3_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2Q8G4_A2Q8G4_ASPNC_425011 and tr_A0A319A1Q3_A0A319A1Q3_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F7HR87_F7HR87_MACMU_9544 and tr_A0A2K5MZP6_A0A2K5MZP6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7XPB1_G7XPB1_ASPKW_1033177 and tr_A0A146FP48_A0A146FP48_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_I1NPS5_I1NPS5_ORYGL_4538 and tr_A0A0D3ERD0_A0A0D3ERD0_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1PB43_I1PB43_ORYGL_4538 and sp_Q10LR9_DCUP2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0MZE6_A0A0E0MZE6_ORYRU_4529 and sp_Q9AXB0_DCUP1_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F2SUF4_F2SUF4_TRIRC_559305 and tr_A0A178F5Q8_A0A178F5Q8_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_N4UKF5_N4UKF5_FUSC1_1229664 and tr_A0A2H3SUM3_A0A2H3SUM3_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_M2S764_M2S764_COCSN_665912 and tr_W6ZCQ8_W6ZCQ8_COCMI_930090 are exactly identical!
WARNING: Sequences tr_V2XLN1_V2XLN1_MONRO_1381753 and tr_A0A0W0FKU8_A0A0W0FKU8_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2QLD5_W2QLD5_PHYPN_761204 and tr_A0A0W8D058_A0A0W8D058_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QLD5_W2QLD5_PHYPN_761204 and tr_W2LRH5_W2LRH5_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A067E0A9_A0A067E0A9_CITSI_2711 and tr_V4SMU2_V4SMU2_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A094F6Q3_A0A094F6Q3_9PEZI_1420912 and tr_A0A1B8G8H3_A0A1B8G8H3_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A117NPJ5_A0A117NPJ5_9EURO_48697 and tr_A0A1V6NIA8_A0A1V6NIA8_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A1S3XTT0_A0A1S3XTT0_TOBAC_4097 and tr_A0A1U7WKB1_A0A1U7WKB1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2K6B4B1_A0A2K6B4B1_MACNE_9545 and tr_A0A2K5ZHR7_A0A2K5ZHR7_MANLE_9568 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/020621_run/phylogeny-snakemake/results/P06132/4_raxmlng_ancestral/P06132.raxml.reduced.phy

Alignment comprises 1 partitions and 367 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 367
Gaps: 5.74 %
Invariant sites: 1.63 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06132/4_raxmlng_ancestral/P06132.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/P06132/3_mltree/P06132.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 92 / 7360
[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: -162787.969247

[00:00:00 -162787.969247] Initial branch length optimization
[00:00:00 -162679.280178] Model parameter optimization (eps = 0.100000)

[00:00:20] Tree #1, final logLikelihood: -162392.751427


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.172096,0.197766) (0.300248,0.355484) (0.287848,0.947325) (0.239808,2.445900) 
   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/P06132/4_raxmlng_ancestral/P06132.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06132/4_raxmlng_ancestral/P06132.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06132/4_raxmlng_ancestral/P06132.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06132/4_raxmlng_ancestral/P06132.raxml.log

Analysis started: 03-Jun-2021 02:44:23 / finished: 03-Jun-2021 02:44:48

Elapsed time: 24.379 seconds

Consumed energy: 1.869 Wh