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 13:37:12 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55211/2_msa/P55211_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55211/3_mltree/P55211.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55211/4_raxmlng_ancestral/P55211 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622803032
  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/P55211/2_msa/P55211_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 416 sites

WARNING: Sequences tr_F1NP15_F1NP15_CHICK_9031 and sp_Q98943_CASP2_CHICK_9031 are exactly identical!
WARNING: Sequences tr_G3QLZ6_G3QLZ6_GORGO_9595 and tr_H2QVJ4_H2QVJ4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QLZ6_G3QLZ6_GORGO_9595 and sp_P42575_CASP2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QLZ6_G3QLZ6_GORGO_9595 and tr_A0A2R9A1X3_A0A2R9A1X3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q29B47_Q29B47_DROPS_46245 and tr_B4GZ35_B4GZ35_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A2I3SBZ3_A0A2I3SBZ3_PANTR_9598 and tr_A0A2R9BDG5_A0A2R9BDG5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TJU8_A0A2I3TJU8_PANTR_9598 and tr_A0A2R9CK75_A0A2R9CK75_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7B3Z2_K7B3Z2_PANTR_9598 and tr_A0A2R9BHM8_A0A2R9BHM8_PANPA_9597 are exactly identical!
WARNING: Sequences sp_Q5IS54_CASP3_PANTR_9598 and sp_P42574_CASP3_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_Q5IS54_CASP3_PANTR_9598 and tr_A0A2R9A7H9_A0A2R9A7H9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7C587_F7C587_MACMU_9544 and tr_A0A096MXQ3_A0A096MXQ3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7GYT8_F7GYT8_MACMU_9544 and tr_G7P629_G7P629_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7GYT8_F7GYT8_MACMU_9544 and tr_A0A2K6BC68_A0A2K6BC68_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7MN58_G7MN58_MACMU_9544 and tr_G7P1H8_G7P1H8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7MN58_G7MN58_MACMU_9544 and tr_A0A096MTV4_A0A096MTV4_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7MN58_G7MN58_MACMU_9544 and tr_A0A2K6DUM6_A0A2K6DUM6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7MN58_G7MN58_MACMU_9544 and tr_A0A2K5YSN9_A0A2K5YSN9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A8WQR6_A8WQR6_CAEBR_6238 and tr_A0A2G5U6X1_A0A2G5U6X1_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_G3X702_G3X702_BOVIN_9913 and sp_Q3T0P5_CASP6_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A096MZW9_A0A096MZW9_PAPAN_9555 and tr_A0A0D9S2F1_A0A0D9S2F1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096MZW9_A0A096MZW9_PAPAN_9555 and tr_A0A2K5LBI6_A0A2K5LBI6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096MZW9_A0A096MZW9_PAPAN_9555 and tr_A0A2K5Y0W1_A0A2K5Y0W1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A1S3ICL7_A0A1S3ICL7_LINUN_7574 and tr_A0A1S3KE01_A0A1S3KE01_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1U7Q288_A0A1U7Q288_MESAU_10036 and sp_Q60431_CASP3_MESAU_10036 are exactly identical!
WARNING: Sequences tr_A0A1U7Q2E9_A0A1U7Q2E9_MESAU_10036 and sp_P55214_CASP7_MESAU_10036 are exactly identical!
WARNING: Sequences tr_A0A226N328_A0A226N328_CALSU_9009 and tr_A0A226PS66_A0A226PS66_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0R6N0_A0A2D0R6N0_ICTPU_7998 and tr_A0A2D0R861_A0A2D0R861_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U3V2B6_A0A2U3V2B6_TURTR_9739 and tr_A0A2Y9N5D6_A0A2Y9N5D6_DELLE_9749 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/P55211/4_raxmlng_ancestral/P55211.raxml.reduced.phy

Alignment comprises 1 partitions and 416 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 416
Gaps: 35.41 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55211/4_raxmlng_ancestral/P55211.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/P55211/3_mltree/P55211.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 104 / 8320
[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: -223486.009455

[00:00:00 -223486.009455] Initial branch length optimization
[00:00:01 -221630.116605] Model parameter optimization (eps = 0.100000)

[00:00:50] Tree #1, final logLikelihood: -220859.552981


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.105961,0.341434) (0.134441,0.311594) (0.305398,0.704852) (0.454200,1.555856) 
   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/P55211/4_raxmlng_ancestral/P55211.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55211/4_raxmlng_ancestral/P55211.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55211/4_raxmlng_ancestral/P55211.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55211/4_raxmlng_ancestral/P55211.raxml.log

Analysis started: 04-Jun-2021 13:37:12 / finished: 04-Jun-2021 13:38:06

Elapsed time: 54.165 seconds