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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 02-Jun-2021 18:03:03 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14393/2_msa/Q14393_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14393/3_mltree/Q14393.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14393/4_raxmlng_ancestral/Q14393 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622646183
  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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14393/2_msa/Q14393_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 678 sites

WARNING: Sequences tr_F1NWP1_F1NWP1_CHICK_9031 and sp_Q804X6_FA9_CHICK_9031 are exactly identical!
WARNING: Sequences tr_M3XTC2_M3XTC2_MUSPF_9669 and tr_A0A2Y9JGB3_A0A2Y9JGB3_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A2J8XCL5_A0A2J8XCL5_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_H2REY4_H2REY4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and sp_Q12805_FBLN3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_G7NA36_G7NA36_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A096NP06_A0A096NP06_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A0D9RPF4_A0A0D9RPF4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A2K5KXY1_A0A2K5KXY1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A2K6DZ29_A0A2K6DZ29_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A2K5YW69_A0A2K5YW69_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A2R9AUY9_A0A2R9AUY9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3S458_G3S458_GORGO_9595 and sp_Q8N2S1_LTBP4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q7T9_H2Q7T9_PANTR_9598 and sp_P00742_FA10_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q7T9_H2Q7T9_PANTR_9598 and tr_A0A2R9B696_A0A2R9B696_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5PSC8_W5PSC8_SHEEP_9940 and tr_Q2KJ89_Q2KJ89_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A0A0MWE2_A0A0A0MWE2_PAPAN_9555 and tr_A0A2K5L0F9_A0A2K5L0F9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0A0MWE2_A0A0A0MWE2_PAPAN_9555 and tr_A0A2K6A267_A0A2K6A267_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3MQ48_A0A2I3MQ48_PAPAN_9555 and tr_A0A2K5LFG6_A0A2K5LFG6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3MQ48_A0A2I3MQ48_PAPAN_9555 and tr_A0A2K6CT24_A0A2K6CT24_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A091VWF1_A0A091VWF1_OPIHO_30419 and tr_A0A0A0A4P3_A0A0A0A4P3_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0V0X293_A0A0V0X293_9BILA_92179 and tr_A0A0V1L600_A0A0V1L600_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0UQZ3_A0A0V0UQZ3_9BILA_181606 and tr_A0A0V0ZS65_A0A0V0ZS65_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0UQZ3_A0A0V0UQZ3_9BILA_181606 and tr_A0A0V1P4F3_A0A0V1P4F3_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0UQZ3_A0A0V0UQZ3_9BILA_181606 and tr_A0A0V0TJX0_A0A0V0TJX0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A2U4BY46_A0A2U4BY46_TURTR_9739 and tr_A0A2Y9Q5P9_A0A2Y9Q5P9_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U3W686_A0A2U3W686_ODORO_9708 and tr_A0A2U3XXH9_A0A2U3XXH9_LEPWE_9713 are exactly identical!
WARNING: Duplicate sequences found: 27

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14393/4_raxmlng_ancestral/Q14393.raxml.reduced.phy

Alignment comprises 1 partitions and 678 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 678
Gaps: 46.84 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14393/4_raxmlng_ancestral/Q14393.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14393/3_mltree/Q14393.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 170 / 13600
[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: -248741.561337

[00:00:00 -248741.561337] Initial branch length optimization
[00:00:02 -247859.446730] Model parameter optimization (eps = 0.100000)

[00:01:03] Tree #1, final logLikelihood: -247068.644033


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.109609,0.224965) (0.085048,0.615027) (0.530501,0.915393) (0.274841,1.591529) 
   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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14393/4_raxmlng_ancestral/Q14393.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14393/4_raxmlng_ancestral/Q14393.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14393/4_raxmlng_ancestral/Q14393.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14393/4_raxmlng_ancestral/Q14393.raxml.log

Analysis started: 02-Jun-2021 18:03:03 / finished: 02-Jun-2021 18:04:14

Elapsed time: 70.433 seconds

Consumed energy: 4.638 Wh