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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 04-Jun-2021 14:12:40 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P48728/2_msa/P48728_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P48728/3_mltree/P48728.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P48728/4_raxmlng_ancestral/P48728 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622805160
  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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P48728/2_msa/P48728_nogap_msa.fasta
[00:00:00] Loaded alignment with 945 taxa and 403 sites

WARNING: Sequences tr_Q4Q134_Q4Q134_LEIMA_5664 and tr_Q4Q135_Q4Q135_LEIMA_5664 are exactly identical!
WARNING: Sequences tr_A0A0D8JTJ0_A0A0D8JTJ0_COCIM_246410 and tr_A0A0J6Y611_A0A0J6Y611_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QQL7_B6QQL7_TALMQ_441960 and tr_A0A093XQW8_A0A093XQW8_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B8NJS4_B8NJS4_ASPFN_332952 and tr_A0A1S9DJB2_A0A1S9DJB2_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UVW9_A0A179UVW9_BLAGS_559298 and tr_C5GCQ1_C5GCQ1_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9FQN2_F9FQN2_FUSOF_660025 and tr_N4TVW9_N4TVW9_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FQN2_F9FQN2_FUSOF_660025 and tr_X0C6E6_X0C6E6_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0E0H666_A0A0E0H666_ORYNI_4536 and tr_I1PQ18_I1PQ18_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0H666_A0A0E0H666_ORYNI_4536 and tr_A0A0D3G0K7_A0A0D3G0K7_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0H666_A0A0E0H666_ORYNI_4536 and tr_Q7XPR2_Q7XPR2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A2QQM8_A2QQM8_ASPNC_425011 and tr_G3YGI8_G3YGI8_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QQM8_A2QQM8_ASPNC_425011 and tr_A0A319AHL7_A0A319AHL7_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A0A1D5QX71_A0A1D5QX71_MACMU_9544 and tr_Q2PFU7_Q2PFU7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QX71_A0A1D5QX71_MACMU_9544 and tr_A0A2K5NDI5_A0A2K5NDI5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QX71_A0A1D5QX71_MACMU_9544 and tr_A0A2K6E7W6_A0A2K6E7W6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QX71_A0A1D5QX71_MACMU_9544 and tr_A0A2K5Z1I9_A0A2K5Z1I9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7XRL2_G7XRL2_ASPKW_1033177 and tr_A0A146FUD6_A0A146FUD6_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F4P419_F4P419_BATDJ_684364 and tr_A0A177WFM6_A0A177WFM6_BATDE_403673 are exactly identical!
WARNING: Sequences tr_A0A0E0PEA5_A0A0E0PEA5_ORYRU_4529 and tr_A0A0D9ZQX4_A0A0D9ZQX4_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_F9WYF5_F9WYF5_ZYMTI_336722 and tr_A0A1X7RGS1_A0A1X7RGS1_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YBH4_G2YBH4_BOTF4_999810 and tr_M7UV74_M7UV74_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SZF1_F2SZF1_TRIRC_559305 and tr_A0A178F489_A0A178F489_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_F2PMW1_F2PMW1_TRIEC_559882 and tr_A0A059IXC5_A0A059IXC5_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_W2PFT4_W2PFT4_PHYPN_761204 and tr_W2JQ52_W2JQ52_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A094ENQ3_A0A094ENQ3_9PEZI_1420912 and tr_A0A2P2SYE3_A0A2P2SYE3_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_V4W9M5_V4W9M5_9ROSI_85681 and tr_A0A2H5N4P5_A0A2H5N4P5_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0F8U578_A0A0F8U578_9EURO_308745 and tr_A0A2T5M209_A0A2T5M209_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0A1N5M4_A0A0A1N5M4_9FUNG_58291 and tr_A0A367JDU2_A0A367JDU2_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0V0WPN1_A0A0V0WPN1_9BILA_92179 and tr_A0A0V1KVQ3_A0A0V1KVQ3_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A124BX83_A0A124BX83_ASPNG_5061 and tr_A0A1L9NNF1_A0A1L9NNF1_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1S3Z7S7_A0A1S3Z7S7_TOBAC_4097 and tr_A0A1S4B9H4_A0A1S4B9H4_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S3Z7S7_A0A1S3Z7S7_TOBAC_4097 and tr_A0A1J6IKI6_A0A1J6IKI6_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1S3Z7S7_A0A1S3Z7S7_TOBAC_4097 and tr_A0A1U7X8P5_A0A1U7X8P5_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2V5I8R9_A0A2V5I8R9_9EURO_1450541 and tr_A0A2V5HX77_A0A2V5HX77_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 34

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P48728/4_raxmlng_ancestral/P48728.raxml.reduced.phy

Alignment comprises 1 partitions and 403 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 403
Gaps: 8.16 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P48728/4_raxmlng_ancestral/P48728.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P48728/3_mltree/P48728.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 101 / 8080
[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: -205496.888436

[00:00:00 -205496.888436] Initial branch length optimization
[00:00:00 -204074.541249] Model parameter optimization (eps = 0.100000)

[00:00:21] Tree #1, final logLikelihood: -203397.704432


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.199775,0.298648) (0.268925,0.378233) (0.248310,0.905287) (0.282990,2.169086) 
   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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P48728/4_raxmlng_ancestral/P48728.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P48728/4_raxmlng_ancestral/P48728.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P48728/4_raxmlng_ancestral/P48728.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P48728/4_raxmlng_ancestral/P48728.raxml.log

Analysis started: 04-Jun-2021 14:12:40 / finished: 04-Jun-2021 14:13:05

Elapsed time: 25.309 seconds