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 03-Jun-2021 02:32:39 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NRP7/2_msa/Q9NRP7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NRP7/3_mltree/Q9NRP7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NRP7/4_raxmlng_ancestral/Q9NRP7 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622676759
  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/Q9NRP7/2_msa/Q9NRP7_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1315 sites

WARNING: Sequences tr_A0A2J8JLQ6_A0A2J8JLQ6_PANTR_9598 and tr_A0A2R9C9K6_A0A2R9C9K6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A087ZXW3_A0A087ZXW3_APIME_7460 and tr_A0A2A3EAH8_A0A2A3EAH8_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158ND45_A0A158ND45_ATTCE_12957 and tr_A0A195BM20_A0A195BM20_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F4PCH9_F4PCH9_BATDJ_684364 and tr_A0A177WYS4_A0A177WYS4_BATDE_403673 are exactly identical!
WARNING: Sequences tr_E6R4V7_E6R4V7_CRYGW_367775 and tr_A0A095D126_A0A095D126_CRYGR_294750 are exactly identical!
WARNING: Sequences tr_E3QC71_E3QC71_COLGM_645133 and tr_A0A010QFG7_A0A010QFG7_9PEZI_1445577 are exactly identical!
WARNING: Sequences tr_E3QC71_E3QC71_COLGM_645133 and tr_A0A066Y0M0_A0A066Y0M0_COLSU_1173701 are exactly identical!
WARNING: Sequences tr_E3QC71_E3QC71_COLGM_645133 and tr_A0A135V7G9_A0A135V7G9_9PEZI_1209931 are exactly identical!
WARNING: Sequences tr_E3QC71_E3QC71_COLGM_645133 and tr_A0A1G4BMS6_A0A1G4BMS6_9PEZI_1209926 are exactly identical!
WARNING: Sequences tr_G7PZ31_G7PZ31_MACFA_9541 and tr_A0A2K6DC09_A0A2K6DC09_MACNE_9545 are exactly identical!
WARNING: Sequences tr_M7Z8Z3_M7Z8Z3_TRIUA_4572 and tr_A0A3B5Y3I6_A0A3B5Y3I6_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A015IA91_A0A015IA91_9GLOM_1432141 and tr_A0A2I1GMG8_A0A2I1GMG8_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015IA91_A0A015IA91_9GLOM_1432141 and tr_U9U015_U9U015_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0D9RPB2_A0A0D9RPB2_CHLSB_60711 and tr_A0A2K6D6X3_A0A2K6D6X3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_S7RGC3_S7RGC3_GLOTA_670483 and tr_A0A165SS37_A0A165SS37_9HOMO_1314782 are exactly identical!
WARNING: Sequences tr_A0A0D2R5C7_A0A0D2R5C7_GOSRA_29730 and tr_A0A1U8IVT1_A0A1U8IVT1_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0A1N5B8_A0A0A1N5B8_9FUNG_58291 and tr_A0A2G4T1X7_A0A2G4T1X7_9FUNG_1340429 are exactly identical!
WARNING: Sequences tr_A0A0A1N5B8_A0A0A1N5B8_9FUNG_58291 and tr_A0A367J3P4_A0A367J3P4_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0V0VDH2_A0A0V0VDH2_9BILA_181606 and tr_A0A0V0TRI9_A0A0V0TRI9_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S3YXF3_A0A1S3YXF3_TOBAC_4097 and tr_A0A1U7XTN9_A0A1U7XTN9_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4CYY4_A0A1S4CYY4_TOBAC_4097 and tr_A0A1U7YUN1_A0A1U7YUN1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2H3DIR7_A0A2H3DIR7_ARMGA_47427 and tr_A0A284RKH8_A0A284RKH8_9AGAR_47428 are exactly identical!
WARNING: Sequences tr_A0A2G2ZF68_A0A2G2ZF68_CAPAN_4072 and tr_A0A2G3CDW9_A0A2G3CDW9_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2I1GDB1_A0A2I1GDB1_9GLOM_588596 and tr_A0A2H5TG04_A0A2H5TG04_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A383VWV5_A0A383VWV5_TETOB_3088 and tr_A0A383W9E4_A0A383W9E4_TETOB_3088 are exactly identical!
WARNING: Duplicate sequences found: 25

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/Q9NRP7/4_raxmlng_ancestral/Q9NRP7.raxml.reduced.phy

Alignment comprises 1 partitions and 1315 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 1315
Gaps: 56.87 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NRP7/4_raxmlng_ancestral/Q9NRP7.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/Q9NRP7/3_mltree/Q9NRP7.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 329 / 26320
[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: -440174.152791

[00:00:00 -440174.152791] Initial branch length optimization
[00:00:03 -423428.674203] Model parameter optimization (eps = 0.100000)

[00:01:23] Tree #1, final logLikelihood: -422295.281729


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.046131,0.197774) (0.082092,0.230984) (0.410467,0.702145) (0.461310,1.482100) 
   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/Q9NRP7/4_raxmlng_ancestral/Q9NRP7.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NRP7/4_raxmlng_ancestral/Q9NRP7.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NRP7/4_raxmlng_ancestral/Q9NRP7.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NRP7/4_raxmlng_ancestral/Q9NRP7.raxml.log

Analysis started: 03-Jun-2021 02:32:39 / finished: 03-Jun-2021 02:34:15

Elapsed time: 95.940 seconds

Consumed energy: 6.198 Wh