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 14:53:17 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20711/2_msa/P20711_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20711/3_mltree/P20711.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20711/4_raxmlng_ancestral/P20711 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622634797
  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/P20711/2_msa/P20711_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 480 sites

WARNING: Sequences tr_B4QDB2_B4QDB2_DROSI_7240 and tr_B4HPX1_B4HPX1_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B2WIZ3_B2WIZ3_PYRTR_426418 and tr_A0A2W1FY95_A0A2W1FY95_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G3S6Z9_G3S6Z9_GORGO_9595 and tr_H2NN75_H2NN75_PONAB_9601 are exactly identical!
WARNING: Sequences tr_Q290I6_Q290I6_DROPS_46245 and tr_B4GBT2_B4GBT2_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q292Z7_Q292Z7_DROPS_46245 and tr_B4GC72_B4GC72_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q29CL0_Q29CL0_DROPS_46245 and tr_B4GXE1_B4GXE1_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A2I3TP36_A0A2I3TP36_PANTR_9598 and tr_A0A2R9A646_A0A2R9A646_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q9E8_H2Q9E8_PANTR_9598 and tr_A0A2R9BKH8_A0A2R9BKH8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9G6X4_F9G6X4_FUSOF_660025 and tr_N4UCT7_N4UCT7_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9G6X4_F9G6X4_FUSOF_660025 and tr_A0A2H3STT7_A0A2H3STT7_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9G6X4_F9G6X4_FUSOF_660025 and tr_A0A2H3G0W7_A0A2H3G0W7_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A088AVR6_A0A088AVR6_APIME_7460 and tr_A0A2A3EPQ8_A0A2A3EPQ8_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NCJ2_A0A158NCJ2_ATTCE_12957 and tr_A0A195BWL8_A0A195BWL8_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NRM3_A0A158NRM3_ATTCE_12957 and tr_A0A195AU70_A0A195AU70_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F4WX52_F4WX52_ACREC_103372 and tr_A0A195F967_A0A195F967_9HYME_34720 are exactly identical!
WARNING: Sequences tr_E3LGP0_E3LGP0_CAERE_31234 and tr_A0A261C2S0_A0A261C2S0_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_A8WNB9_A8WNB9_CAEBR_6238 and tr_A0A2G5UXU4_A0A2G5UXU4_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_M4F5W0_M4F5W0_BRARP_51351 and tr_A0A078H2E5_A0A078H2E5_BRANA_3708 are exactly identical!
WARNING: Sequences tr_D7NYN0_D7NYN0_CITSI_2711 and tr_V4VDK5_V4VDK5_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A2I3MBM0_A0A2I3MBM0_PAPAN_9555 and tr_A0A0D9REQ3_A0A0D9REQ3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3MBM0_A0A2I3MBM0_PAPAN_9555 and tr_A0A2K5NPK6_A0A2K5NPK6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3MBM0_A0A2I3MBM0_PAPAN_9555 and tr_A0A2K6AZC6_A0A2K6AZC6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3MBM0_A0A2I3MBM0_PAPAN_9555 and tr_A0A2K5Y533_A0A2K5Y533_MANLE_9568 are exactly identical!
WARNING: Sequences tr_V4T407_V4T407_9ROSI_85681 and tr_A0A2H5NHE0_A0A2H5NHE0_CITUN_55188 are exactly identical!
WARNING: Sequences tr_V4U0J4_V4U0J4_9ROSI_85681 and tr_A0A2H5P3Y1_A0A2H5P3Y1_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A1S4A0G2_A0A1S4A0G2_TOBAC_4097 and tr_A0A1U7UXF3_A0A1U7UXF3_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2P5CWQ7_A0A2P5CWQ7_PARAD_3476 and tr_A0A2P5CWT6_A0A2P5CWT6_PARAD_3476 are exactly identical!
WARNING: Duplicate sequences found: 27

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/P20711/4_raxmlng_ancestral/P20711.raxml.reduced.phy

Alignment comprises 1 partitions and 480 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 480
Gaps: 3.55 %
Invariant sites: 0.21 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20711/4_raxmlng_ancestral/P20711.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/P20711/3_mltree/P20711.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 120 / 9600
[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: -231086.586945

[00:00:00 -231086.586945] Initial branch length optimization
[00:00:01 -230939.429712] Model parameter optimization (eps = 0.100000)

[00:00:30] Tree #1, final logLikelihood: -230384.550203


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.195564,0.354951) (0.357120,0.449949) (0.246782,1.045583) (0.200535,2.552518) 
   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/P20711/4_raxmlng_ancestral/P20711.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20711/4_raxmlng_ancestral/P20711.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20711/4_raxmlng_ancestral/P20711.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P20711/4_raxmlng_ancestral/P20711.raxml.log

Analysis started: 02-Jun-2021 14:53:17 / finished: 02-Jun-2021 14:53:52

Elapsed time: 34.400 seconds