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 02-Jun-2021 18:11:00 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49736/2_msa/P49736_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49736/3_mltree/P49736.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49736/4_raxmlng_ancestral/P49736 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622646660
  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/P49736/2_msa/P49736_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 904 sites

WARNING: Sequences tr_A0A0E1RZM0_A0A0E1RZM0_COCIM_246410 and tr_A0A0J7ARM5_A0A0J7ARM5_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6Q3C1_B6Q3C1_TALMQ_441960 and tr_A0A093VMJ3_A0A093VMJ3_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2VT27_B2VT27_PYRTR_426418 and tr_A0A2W1H7P3_A0A2W1H7P3_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_C0NPQ6_C0NPQ6_AJECG_447093 and tr_F0UP88_F0UP88_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A179UUD5_A0A179UUD5_BLAGS_559298 and tr_C5GMN3_C5GMN3_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2QNA7_H2QNA7_PANTR_9598 and sp_P49736_MCM2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QNA7_H2QNA7_PANTR_9598 and tr_A0A2R8ZAB9_A0A2R8ZAB9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9F4F7_F9F4F7_FUSOF_660025 and tr_A0A0D2Y2U1_A0A0D2Y2U1_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9F4F7_F9F4F7_FUSOF_660025 and tr_N4UTF0_N4UTF0_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9F4F7_F9F4F7_FUSOF_660025 and tr_X0CC55_X0CC55_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A2QU75_A2QU75_ASPNC_425011 and tr_A0A319AL81_A0A319AL81_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F7HLV9_F7HLV9_MACMU_9544 and tr_G7PIZ9_G7PIZ9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7HLV9_F7HLV9_MACMU_9544 and tr_A0A096MXM7_A0A096MXM7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7HLV9_F7HLV9_MACMU_9544 and tr_A0A2K5LCM6_A0A2K5LCM6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7HLV9_F7HLV9_MACMU_9544 and tr_A0A2K6CCM9_A0A2K6CCM9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F4NXZ8_F4NXZ8_BATDJ_684364 and tr_A0A177WLF2_A0A177WLF2_BATDE_403673 are exactly identical!
WARNING: Sequences tr_F9XE61_F9XE61_ZYMTI_336722 and tr_A0A1X7RXR6_A0A1X7RXR6_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YFD6_G2YFD6_BOTF4_999810 and tr_M7UBT0_M7UBT0_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_E3N2S4_E3N2S4_CAERE_31234 and tr_A0A261C2Y9_A0A261C2Y9_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_W2R390_W2R390_PHYPN_761204 and tr_W2KL48_W2KL48_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A094F5Y8_A0A094F5Y8_9PEZI_1420912 and tr_A0A1B8GY89_A0A1B8GY89_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0D2Q0W2_A0A0D2Q0W2_GOSRA_29730 and tr_A0A1U8HW27_A0A1U8HW27_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0F8UX04_A0A0F8UX04_9EURO_308745 and tr_A0A2T5LZ03_A0A2T5LZ03_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0G4P7U1_A0A0G4P7U1_PENCA_1429867 and tr_A0A1V6R5K0_A0A1V6R5K0_9EURO_60172 are exactly identical!
WARNING: Sequences tr_A0A0V1CDG2_A0A0V1CDG2_TRIBR_45882 and tr_A0A0V0TMC2_A0A0V0TMC2_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A100IM53_A0A100IM53_ASPNG_5061 and tr_A0A1L9NFT1_A0A1L9NFT1_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A319C218_A0A319C218_9EURO_1448315 and tr_A0A2V5HY37_A0A2V5HY37_9EURO_1450541 are exactly identical!
WARNING: Sequences tr_A0A319C218_A0A319C218_9EURO_1448315 and tr_A0A2V5HES0_A0A2V5HES0_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 28

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/P49736/4_raxmlng_ancestral/P49736.raxml.reduced.phy

Alignment comprises 1 partitions and 904 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 904
Gaps: 12.98 %
Invariant sites: 1.44 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49736/4_raxmlng_ancestral/P49736.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/P49736/3_mltree/P49736.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 226 / 18080
[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: -306436.119387

[00:00:00 -306436.119387] Initial branch length optimization
[00:00:01 -305825.583528] Model parameter optimization (eps = 0.100000)

[00:00:42] Tree #1, final logLikelihood: -305326.761826


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.213843,0.222676) (0.244858,0.372392) (0.298448,0.945835) (0.242851,2.383832) 
   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/P49736/4_raxmlng_ancestral/P49736.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49736/4_raxmlng_ancestral/P49736.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49736/4_raxmlng_ancestral/P49736.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49736/4_raxmlng_ancestral/P49736.raxml.log

Analysis started: 02-Jun-2021 18:11:00 / finished: 02-Jun-2021 18:11:51

Elapsed time: 51.493 seconds

Consumed energy: 2.114 Wh