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 18:22:32 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15911/2_msa/Q15911_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15911/3_mltree/Q15911.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15911/4_raxmlng_ancestral/Q15911 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622647352
  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/Q15911/2_msa/Q15911_nogap_msa.fasta
[00:00:00] Loaded alignment with 907 taxa and 3703 sites

WARNING: Sequences sp_O88609_LMX1B_MOUSE_10090 and tr_M3YR06_M3YR06_MUSPF_9669 are exactly identical!
WARNING: Sequences sp_O88609_LMX1B_MOUSE_10090 and tr_I3NEG6_I3NEG6_ICTTR_43179 are exactly identical!
WARNING: Sequences sp_O88609_LMX1B_MOUSE_10090 and tr_A0A2R8PA11_A0A2R8PA11_CALJA_9483 are exactly identical!
WARNING: Sequences sp_O88609_LMX1B_MOUSE_10090 and tr_A0A286ZUN2_A0A286ZUN2_PIG_9823 are exactly identical!
WARNING: Sequences tr_A0A2I3GL84_A0A2I3GL84_NOMLE_61853 and tr_G3SJ98_G3SJ98_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3GL84_A0A2I3GL84_NOMLE_61853 and tr_A0A2I3S5M9_A0A2I3S5M9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3GL84_A0A2I3GL84_NOMLE_61853 and tr_A0A2R9BAU6_A0A2R9BAU6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2N712_H2N712_PONAB_9601 and sp_Q68G74_LHX8_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PTF0_H2PTF0_PONAB_9601 and tr_G3TF87_G3TF87_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_H0WI04_H0WI04_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and sp_O60663_LMX1B_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_D2H3X4_D2H3X4_AILME_9646 are exactly identical!
WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_A0A0D9RMI6_A0A0D9RMI6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_A0A2K6C4K9_A0A2K6C4K9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_A0A2Y9NL89_A0A2Y9NL89_DELLE_9749 are exactly identical!
WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_A0A2Y9T224_A0A2Y9T224_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_E3MG77_E3MG77_CAERE_31234 and tr_A0A261AT74_A0A261AT74_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_G1L9U3_G1L9U3_AILME_9646 and tr_A0A384C241_A0A384C241_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A2I3LDJ2_A0A2I3LDJ2_PAPAN_9555 and tr_A0A2K5MVV3_A0A2K5MVV3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3LDJ2_A0A2I3LDJ2_PAPAN_9555 and tr_A0A2K6AYA2_A0A2K6AYA2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A091UU84_A0A091UU84_NIPNI_128390 and tr_A0A087RDS5_A0A087RDS5_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091UU84_A0A091UU84_NIPNI_128390 and tr_A0A091WNC9_A0A091WNC9_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091UU84_A0A091UU84_NIPNI_128390 and tr_A0A0A0AEQ5_A0A0A0AEQ5_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A1S3T1R2_A0A1S3T1R2_SALSA_8030 and tr_A0A060Y7L0_A0A060Y7L0_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1I7THM1_A0A1I7THM1_9PELO_1561998 and tr_A0A1I7THM2_A0A1I7THM2_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A226NB76_A0A226NB76_CALSU_9009 and tr_A0A226PI53_A0A226PI53_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2U4A1B0_A0A2U4A1B0_TURTR_9739 and tr_A0A2Y9NUF7_A0A2Y9NUF7_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4A1B0_A0A2U4A1B0_TURTR_9739 and tr_A0A2Y9F546_A0A2Y9F546_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U4A1B0_A0A2U4A1B0_TURTR_9739 and tr_A0A384A6X9_A0A384A6X9_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A2Y9NTG7_A0A2Y9NTG7_DELLE_9749 and tr_A0A2Y9SU71_A0A2Y9SU71_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 30

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/Q15911/4_raxmlng_ancestral/Q15911.raxml.reduced.phy

Alignment comprises 1 partitions and 3703 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 3703
Gaps: 68.27 %
Invariant sites: 0.08 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15911/4_raxmlng_ancestral/Q15911.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/Q15911/3_mltree/Q15911.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 926 / 74080
[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: -1300695.779504

[00:00:01 -1300695.779504] Initial branch length optimization
[00:00:11 -646186.497743] Model parameter optimization (eps = 0.100000)

[00:09:15] Tree #1, final logLikelihood: -641914.290848


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.204136,0.389906) (0.173684,1.128567) (0.299981,0.587398) (0.322199,1.701383) 
   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/Q15911/4_raxmlng_ancestral/Q15911.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15911/4_raxmlng_ancestral/Q15911.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15911/4_raxmlng_ancestral/Q15911.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15911/4_raxmlng_ancestral/Q15911.raxml.log

Analysis started: 02-Jun-2021 18:22:32 / finished: 02-Jun-2021 18:32:20

Elapsed time: 587.561 seconds

Consumed energy: 34.555 Wh