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 18:36:18 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15046/2_msa/Q15046_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15046/3_mltree/Q15046.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15046/4_raxmlng_ancestral/Q15046 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622648178
  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/Q15046/2_msa/Q15046_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 597 sites

WARNING: Sequences tr_J3KIX5_J3KIX5_COCIM_246410 and tr_E9CWP8_E9CWP8_COCPS_443226 are exactly identical!
WARNING: Sequences tr_J3KIX5_J3KIX5_COCIM_246410 and tr_A0A0J6Y2M3_A0A0J6Y2M3_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B8N2E2_B8N2E2_ASPFN_332952 and tr_Q2UM12_Q2UM12_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8N2E2_B8N2E2_ASPFN_332952 and tr_A0A1S9DNZ9_A0A1S9DNZ9_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_J5K1T7_J5K1T7_BEAB2_655819 and tr_A0A0A2VQZ0_A0A0A2VQZ0_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J5K1T7_J5K1T7_BEAB2_655819 and tr_A0A2N6NBZ8_A0A2N6NBZ8_BEABA_176275 are exactly identical!
WARNING: Sequences tr_A2QVR8_A2QVR8_ASPNC_425011 and tr_G3YCB9_G3YCB9_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QVR8_A2QVR8_ASPNC_425011 and tr_A0A319ABU0_A0A319ABU0_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XAR1_G7XAR1_ASPKW_1033177 and tr_A0A146F889_A0A146F889_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F9X9K6_F9X9K6_ZYMTI_336722 and tr_A0A1X7RQZ9_A0A1X7RQZ9_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YA13_G2YA13_BOTF4_999810 and tr_M7TWK6_M7TWK6_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SDN0_F2SDN0_TRIRC_559305 and tr_A0A178EUK3_A0A178EUK3_TRIRU_5551 are exactly identical!
WARNING: Sequences sp_C4V8R9_SYKC_NOSCE_578460 and tr_A0A0F9WT61_A0A0F9WT61_9MICR_40302 are exactly identical!
WARNING: Sequences tr_A0A0D2XGH5_A0A0D2XGH5_FUSO4_426428 and tr_N4TWK8_N4TWK8_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_A0A0D2XGH5_A0A0D2XGH5_FUSO4_426428 and tr_X0CYS8_X0CYS8_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0D2XGH5_A0A0D2XGH5_FUSO4_426428 and tr_A0A2H3TLG5_A0A2H3TLG5_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A0A0D2XGH5_A0A0D2XGH5_FUSO4_426428 and tr_A0A2H3GQ05_A0A2H3GQ05_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_L0PFG7_L0PFG7_PNEJ8_1209962 and tr_A0A0W4ZJZ4_A0A0W4ZJZ4_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_V2X850_V2X850_MONRO_1381753 and tr_A0A0W0G2A4_A0A0W0G2A4_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2PZ86_W2PZ86_PHYPN_761204 and tr_A0A0W8BXR3_A0A0W8BXR3_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PZ86_W2PZ86_PHYPN_761204 and tr_W2KR19_W2KR19_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2QT19_W2QT19_PHYPN_761204 and tr_A0A0W8BV24_A0A0W8BV24_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QT19_W2QT19_PHYPN_761204 and tr_W2K1H5_W2K1H5_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015LVJ2_A0A015LVJ2_9GLOM_1432141 and tr_U9SY06_U9SY06_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2K6VV83_A0A2K6VV83_ONCVO_6282 and tr_A0A182E3S1_A0A182E3S1_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A094E487_A0A094E487_9PEZI_1420912 and tr_A0A1B8GW11_A0A1B8GW11_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0B4HX38_A0A0B4HX38_METMF_1276143 and tr_A0A0D9NPK0_A0A0D9NPK0_METAN_1291518 are exactly identical!
WARNING: Sequences tr_A0A0D2USQ2_A0A0D2USQ2_GOSRA_29730 and tr_A0A1U8KEE3_A0A1U8KEE3_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0F8WD90_A0A0F8WD90_9EURO_308745 and tr_A0A2T5M752_A0A2T5M752_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_V6RRH2_V6RRH2_GIBZE_229533 and tr_A0A2T4GJB9_A0A2T4GJB9_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A1S4C181_A0A1S4C181_TOBAC_4097 and tr_A0A1U7V511_A0A1U7V511_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3IIR5_A0A1S3IIR5_LINUN_7574 and tr_A0A1S3J2I6_A0A1S3J2I6_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1J1J545_A0A1J1J545_9DIPT_568069 and tr_A0A1J1J949_A0A1J1J949_9DIPT_568069 are exactly identical!
WARNING: Sequences tr_A0A1L9X1P4_A0A1L9X1P4_ASPAC_690307 and tr_A0A319BZG7_A0A319BZG7_9EURO_1448315 are exactly identical!
WARNING: Sequences tr_A0A2V5IG77_A0A2V5IG77_9EURO_1450541 and tr_A0A2V5I3P3_A0A2V5I3P3_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 35

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/Q15046/4_raxmlng_ancestral/Q15046.raxml.reduced.phy

Alignment comprises 1 partitions and 597 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 597
Gaps: 8.32 %
Invariant sites: 2.18 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15046/4_raxmlng_ancestral/Q15046.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/Q15046/3_mltree/Q15046.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 150 / 12000
[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: -229524.349059

[00:00:00 -229524.349059] Initial branch length optimization
[00:00:02 -229149.646950] Model parameter optimization (eps = 0.100000)

[00:01:05] Tree #1, final logLikelihood: -228628.397740


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.195864,0.265671) (0.296765,0.459200) (0.243277,0.824406) (0.264094,2.314069) 
   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/Q15046/4_raxmlng_ancestral/Q15046.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15046/4_raxmlng_ancestral/Q15046.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15046/4_raxmlng_ancestral/Q15046.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15046/4_raxmlng_ancestral/Q15046.raxml.log

Analysis started: 02-Jun-2021 18:36:18 / finished: 02-Jun-2021 18:37:29

Elapsed time: 70.998 seconds

Consumed energy: 4.069 Wh