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 14:08:51 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H4A3/2_msa/Q9H4A3_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H4A3/3_mltree/Q9H4A3.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H4A3/4_raxmlng_ancestral/Q9H4A3 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622632131
  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/Q9H4A3/2_msa/Q9H4A3_nogap_msa.fasta
[00:00:00] Loaded alignment with 997 taxa and 2382 sites

WARNING: Sequences tr_D8T299_D8T299_SELML_88036 and tr_D8T849_D8T849_SELML_88036 are exactly identical!
WARNING: Sequences tr_A0A0E0GB60_A0A0E0GB60_ORYNI_4536 and tr_I1P316_I1P316_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0GB60_A0A0E0GB60_ORYNI_4536 and tr_A0A0E0NJ35_A0A0E0NJ35_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GB60_A0A0E0GB60_ORYNI_4536 and tr_A0A0D3F8S3_A0A0D3F8S3_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0H8F6_A0A0E0H8F6_ORYNI_4536 and tr_A0A0E0PGH6_A0A0E0PGH6_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0H8F6_A0A0E0H8F6_ORYNI_4536 and tr_A0A0D9ZT92_A0A0D9ZT92_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A2ZBQ8_A2ZBQ8_ORYSI_39946 and tr_I1QXX1_I1QXX1_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A2ZBQ8_A2ZBQ8_ORYSI_39946 and tr_A0A0E0BFM1_A0A0E0BFM1_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A2ZBQ8_A2ZBQ8_ORYSI_39946 and sp_Q2RA93_WNK6_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_B8AWX6_B8AWX6_ORYSI_39946 and sp_Q65X23_WNK2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1R4A9_I1R4A9_ORYGL_4538 and tr_A0A0E0RE52_A0A0E0RE52_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1R4A9_I1R4A9_ORYGL_4538 and tr_A0A0E0BPC6_A0A0E0BPC6_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_M4F902_M4F902_BRARP_51351 and tr_A0A078FVW8_A0A078FVW8_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4FH36_M4FH36_BRARP_51351 and tr_A0A078IIB7_A0A078IIB7_BRANA_3708 are exactly identical!
WARNING: Sequences tr_W2R8T0_W2R8T0_PHYPN_761204 and tr_A0A0W8CDV5_A0A0W8CDV5_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A067H6I0_A0A067H6I0_CITSI_2711 and tr_V4TCI4_V4TCI4_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A078J617_A0A078J617_BRANA_3708 and tr_A0A0D3E108_A0A0D3E108_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A078JFQ9_A0A078JFQ9_BRANA_3708 and tr_A0A0D3ACH7_A0A0D3ACH7_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A078JT25_A0A078JT25_BRANA_3708 and tr_A0A0D3B2U8_A0A0D3B2U8_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0A1N9C6_A0A0A1N9C6_9FUNG_58291 and tr_A0A367K9F6_A0A367K9F6_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A1S3ZAN5_A0A1S3ZAN5_TOBAC_4097 and tr_A0A1U7V6V5_A0A1U7V6V5_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4A6X4_A0A1S4A6X4_TOBAC_4097 and tr_A0A1U7VHU4_A0A1U7VHU4_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A226NCM3_A0A226NCM3_CALSU_9009 and tr_A0A226PU95_A0A226PU95_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0PVB7_A0A2D0PVB7_ICTPU_7998 and tr_A0A2D0PVC2_A0A2D0PVC2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0R0H3_A0A2D0R0H3_ICTPU_7998 and tr_A0A2D0R2V7_A0A2D0R2V7_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 25

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/Q9H4A3/4_raxmlng_ancestral/Q9H4A3.raxml.reduced.phy

Alignment comprises 1 partitions and 2382 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 2382
Gaps: 63.09 %
Invariant sites: 0.13 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H4A3/4_raxmlng_ancestral/Q9H4A3.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/Q9H4A3/3_mltree/Q9H4A3.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 596 / 47680
[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: -1044936.669674

[00:00:00 -1044936.669674] Initial branch length optimization
[00:00:07 -674235.155407] Model parameter optimization (eps = 0.100000)

[00:03:23] Tree #1, final logLikelihood: -672763.534413


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.063674,0.098200) (0.052867,0.141627) (0.248173,0.522550) (0.635286,1.348333) 
   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/Q9H4A3/4_raxmlng_ancestral/Q9H4A3.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H4A3/4_raxmlng_ancestral/Q9H4A3.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H4A3/4_raxmlng_ancestral/Q9H4A3.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H4A3/4_raxmlng_ancestral/Q9H4A3.raxml.log

Analysis started: 02-Jun-2021 14:08:51 / finished: 02-Jun-2021 14:12:35

Elapsed time: 224.484 seconds