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 02-Jun-2021 15:28:35 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13608/2_msa/Q13608_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13608/3_mltree/Q13608.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13608/4_raxmlng_ancestral/Q13608 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622636915
  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/Q13608/2_msa/Q13608_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 980 sites

WARNING: Sequences tr_B6Q6M1_B6Q6M1_TALMQ_441960 and tr_A0A093VMT9_A0A093VMT9_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_F9G521_F9G521_FUSOF_660025 and tr_X0CWK1_X0CWK1_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9G521_F9G521_FUSOF_660025 and tr_A0A2H3THI8_A0A2H3THI8_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_Q2UPU9_Q2UPU9_ASPOR_510516 and tr_A0A1S9DTH6_A0A1S9DTH6_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A2XCL6_A2XCL6_ORYSI_39946 and tr_A0A0E0CVA5_A0A0E0CVA5_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A2XCL6_A2XCL6_ORYSI_39946 and tr_A0A0D3FDX3_A0A0D3FDX3_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A2XCL6_A2XCL6_ORYSI_39946 and tr_A0A0D9Z263_A0A0D9Z263_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A2XCL6_A2XCL6_ORYSI_39946 and tr_Q10RP0_Q10RP0_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1PPY0_I1PPY0_ORYGL_4538 and tr_A0A0D3G0D8_A0A0D3G0D8_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0PE40_A0A0E0PE40_ORYRU_4529 and tr_Q7XTN8_Q7XTN8_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F9X4C5_F9X4C5_ZYMTI_336722 and tr_A0A0F4GLP0_A0A0F4GLP0_9PEZI_1047168 are exactly identical!
WARNING: Sequences tr_F9X4C5_F9X4C5_ZYMTI_336722 and tr_A0A1X7RJB3_A0A1X7RJB3_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_A8WN57_A8WN57_CAEBR_6238 and tr_A0A2G5UY78_A0A2G5UY78_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_F2SJ81_F2SJ81_TRIRC_559305 and tr_A0A178F2J7_A0A178F2J7_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_V2WTA6_V2WTA6_MONRO_1381753 and tr_A0A0W0FS88_A0A0W0FS88_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2QZZ8_W2QZZ8_PHYPN_761204 and tr_A0A0W8C8X4_A0A0W8C8X4_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QZZ8_W2QZZ8_PHYPN_761204 and tr_W2I822_W2I822_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2QZZ8_W2QZZ8_PHYPN_761204 and tr_A0A329S4K5_A0A329S4K5_9STRA_29920 are exactly identical!
WARNING: Sequences tr_A0A096NI80_A0A096NI80_PAPAN_9555 and tr_A0A2K6DBY4_A0A2K6DBY4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A094EQ43_A0A094EQ43_9PEZI_1420912 and tr_A0A1B8E660_A0A1B8E660_9PEZI_1524831 are exactly identical!
WARNING: Sequences tr_A0A094EQ43_A0A094EQ43_9PEZI_1420912 and tr_A0A1B8GVT3_A0A1B8GVT3_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A094EQ43_A0A094EQ43_9PEZI_1420912 and tr_A0A1B8F0C9_A0A1B8F0C9_9PEZI_1622149 are exactly identical!
WARNING: Sequences tr_A0A0K0FKR9_A0A0K0FKR9_STRVS_75913 and tr_A0A0N5B656_A0A0N5B656_STREA_174720 are exactly identical!
WARNING: Sequences tr_A0A1S3WXP8_A0A1S3WXP8_TOBAC_4097 and tr_A0A1U7X6D0_A0A1U7X6D0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4CL01_A0A1S4CL01_TOBAC_4097 and tr_Q1G0Z1_Q1G0Z1_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A2J6T7G7_A0A2J6T7G7_9HELO_1095630 and tr_A0A2J6RKP9_A0A2J6RKP9_9HELO_1149755 are exactly identical!
WARNING: Sequences tr_A0A2S7PMS8_A0A2S7PMS8_9HELO_2070414 and tr_A0A2S7R3Y3_A0A2S7R3Y3_9HELO_2070412 are exactly identical!
WARNING: Sequences tr_A0A2G4SZJ4_A0A2G4SZJ4_9FUNG_1340429 and tr_A0A367J3D0_A0A367J3D0_9FUNG_86630 are exactly identical!
WARNING: Duplicate sequences found: 28

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/Q13608/4_raxmlng_ancestral/Q13608.raxml.reduced.phy

Alignment comprises 1 partitions and 980 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 980
Gaps: 21.54 %
Invariant sites: 0.82 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13608/4_raxmlng_ancestral/Q13608.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/Q13608/3_mltree/Q13608.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 245 / 19600
[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: -456493.455704

[00:00:00 -456493.455704] Initial branch length optimization
[00:00:02 -452012.673186] Model parameter optimization (eps = 0.100000)

[00:01:38] Tree #1, final logLikelihood: -451472.537702


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.159567,0.216964) (0.198904,0.435669) (0.314936,0.841356) (0.326594,1.879248) 
   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/Q13608/4_raxmlng_ancestral/Q13608.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13608/4_raxmlng_ancestral/Q13608.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13608/4_raxmlng_ancestral/Q13608.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13608/4_raxmlng_ancestral/Q13608.raxml.log

Analysis started: 02-Jun-2021 15:28:35 / finished: 02-Jun-2021 15:30:22

Elapsed time: 107.804 seconds