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 14:07:20 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NP58/2_msa/Q9NP58_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NP58/3_mltree/Q9NP58.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NP58/4_raxmlng_ancestral/Q9NP58 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622632040
  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/Q9NP58/2_msa/Q9NP58_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 842 sites

WARNING: Sequences tr_B6QL03_B6QL03_TALMQ_441960 and tr_A0A093UQU0_A0A093UQU0_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WKW0_B2WKW0_PYRTR_426418 and tr_A0A2W1I4B2_A0A2W1I4B2_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_B8NH70_B8NH70_ASPFN_332952 and tr_Q2UED7_Q2UED7_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_K7BWZ4_K7BWZ4_PANTR_9598 and tr_A0A2R9AL60_A0A2R9AL60_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FJC9_F9FJC9_FUSOF_660025 and tr_A0A0D2Y976_A0A0D2Y976_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FJC9_F9FJC9_FUSOF_660025 and tr_X0CQX2_X0CQX2_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FJC9_F9FJC9_FUSOF_660025 and tr_A0A2H3TLS9_A0A2H3TLS9_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A2QSG1_A2QSG1_ASPNC_425011 and tr_A0A319B467_A0A319B467_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A5AAV0_A5AAV0_ASPNC_425011 and tr_G3XZ81_G3XZ81_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_G7NS55_G7NS55_MACMU_9544 and tr_G7Q326_G7Q326_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7NS55_G7NS55_MACMU_9544 and tr_A0A2K5KJY9_A0A2K5KJY9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7NS55_G7NS55_MACMU_9544 and tr_A0A2K5Y8X4_A0A2K5Y8X4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7XF11_G7XF11_ASPKW_1033177 and tr_A0A146F1J7_A0A146F1J7_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XLY2_G7XLY2_ASPKW_1033177 and tr_A0A146FBH1_A0A146FBH1_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G2YR25_G2YR25_BOTF4_999810 and tr_M7TBB8_M7TBB8_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SRA8_F2SRA8_TRIRC_559305 and tr_A0A178EXR7_A0A178EXR7_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_B3RM86_B3RM86_TRIAD_10228 and tr_A0A369SIT8_A0A369SIT8_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G7PK40_G7PK40_MACFA_9541 and tr_A0A096MRT7_A0A096MRT7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PK40_G7PK40_MACFA_9541 and tr_A0A0D9R7A2_A0A0D9R7A2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A0E0A4F3_A0A0E0A4F3_9ORYZ_40148 and tr_Q658I3_Q658I3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A067EIC7_A0A067EIC7_CITSI_2711 and tr_V4SWV6_V4SWV6_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067EIC7_A0A067EIC7_CITSI_2711 and tr_A0A2H5Q2Y4_A0A2H5Q2Y4_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A096MXT6_A0A096MXT6_PAPAN_9555 and tr_A0A2K6DSA7_A0A2K6DSA7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A094EJ35_A0A094EJ35_9PEZI_1420912 and tr_A0A1B8GVW1_A0A1B8GVW1_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A124BWF4_A0A124BWF4_ASPNG_5061 and tr_A0A1L9MYT1_A0A1L9MYT1_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1S4D100_A0A1S4D100_TOBAC_4097 and tr_A0A1U7V1P7_A0A1U7V1P7_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2N5T3Z6_A0A2N5T3Z6_9BASI_200324 and tr_A0A2N5VXV8_A0A2N5VXV8_9BASI_200324 are exactly identical!
WARNING: Sequences tr_A0A2V5J188_A0A2V5J188_9EURO_1450541 and tr_A0A2V5H2R9_A0A2V5H2R9_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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NP58/4_raxmlng_ancestral/Q9NP58.raxml.reduced.phy

Alignment comprises 1 partitions and 842 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 842
Gaps: 16.73 %
Invariant sites: 0.48 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NP58/4_raxmlng_ancestral/Q9NP58.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/Q9NP58/3_mltree/Q9NP58.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 211 / 16880
[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: -369928.321811

[00:00:00 -369928.321811] Initial branch length optimization
[00:00:03 -363273.924561] Model parameter optimization (eps = 0.100000)

[00:00:47] Tree #1, final logLikelihood: -361792.092422


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.173603,0.204523) (0.263479,0.286109) (0.356483,1.183218) (0.206435,2.263727) 
   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/Q9NP58/4_raxmlng_ancestral/Q9NP58.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NP58/4_raxmlng_ancestral/Q9NP58.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NP58/4_raxmlng_ancestral/Q9NP58.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NP58/4_raxmlng_ancestral/Q9NP58.raxml.log

Analysis started: 02-Jun-2021 14:07:20 / finished: 02-Jun-2021 14:08:15

Elapsed time: 55.003 seconds