IMPORTANT WARNING: Sequences KY494475 and KY494525 are exactly identical


IMPORTANT WARNING: Sequences KY494475 and OR005153 are exactly identical


IMPORTANT WARNING: Sequences KY494575 and KY494625 are exactly identical

IMPORTANT WARNING
Found 3 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.

Just in case you might need it, an alignment file with 
sequence duplicates removed is printed to file ITS_out.phy.reduced


Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" 



This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.

With greatly appreciated code contributions by:
Andre Aberer      (HITS)
Simon Berger      (HITS)
Alexey Kozlov     (HITS)
Kassian Kobert    (HITS)
David Dao         (KIT and HITS)
Sarah Lutteropp   (KIT and HITS)
Nick Pattengale   (Sandia)
Wayne Pfeiffer    (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor    (UF)


Alignment has 113 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.00%

RAxML rapid bootstrapping and subsequent ML search

Using 1 distinct models/data partitions with joint branch length optimization



Executing 100 rapid bootstrap inferences and thereafter a thorough ML search 

All free model parameters will be estimated by RAxML
GAMMA model of rate heterogeneity, ML estimate of alpha-parameter

GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units

Partition: 0
Alignment Patterns: 113
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR




RAxML was called as follows:

/opt/biosoft/RAxML-8.2.12/raxmlHPC-PTHREADS-SSE3 -f a -x 12345 -p 12345 -# 100 -m GTRGAMMA -s ITS_out.phy -n out_codon -T 8 



Time for BS model parameter optimization 0.025000
Bootstrap[0]: Time 0.183888 seconds, bootstrap likelihood -1904.565008, best rearrangement setting 13
Bootstrap[1]: Time 0.170812 seconds, bootstrap likelihood -1989.476828, best rearrangement setting 13
Bootstrap[2]: Time 0.143013 seconds, bootstrap likelihood -1688.872645, best rearrangement setting 12
Bootstrap[3]: Time 0.133685 seconds, bootstrap likelihood -1813.913633, best rearrangement setting 15
Bootstrap[4]: Time 0.054981 seconds, bootstrap likelihood -1816.665380, best rearrangement setting 10
Bootstrap[5]: Time 0.065900 seconds, bootstrap likelihood -1827.360407, best rearrangement setting 10
Bootstrap[6]: Time 0.062582 seconds, bootstrap likelihood -1771.450581, best rearrangement setting 6
Bootstrap[7]: Time 0.062668 seconds, bootstrap likelihood -1724.249413, best rearrangement setting 14
Bootstrap[8]: Time 0.055050 seconds, bootstrap likelihood -1723.055636, best rearrangement setting 5
Bootstrap[9]: Time 0.056181 seconds, bootstrap likelihood -1629.869865, best rearrangement setting 7
Bootstrap[10]: Time 0.064395 seconds, bootstrap likelihood -1859.942266, best rearrangement setting 7
Bootstrap[11]: Time 0.052543 seconds, bootstrap likelihood -1763.268767, best rearrangement setting 5
Bootstrap[12]: Time 0.052319 seconds, bootstrap likelihood -1837.516030, best rearrangement setting 8
Bootstrap[13]: Time 0.058522 seconds, bootstrap likelihood -2021.918512, best rearrangement setting 7
Bootstrap[14]: Time 0.062450 seconds, bootstrap likelihood -1698.380620, best rearrangement setting 12
Bootstrap[15]: Time 0.062845 seconds, bootstrap likelihood -1734.616051, best rearrangement setting 15
Bootstrap[16]: Time 0.055275 seconds, bootstrap likelihood -1791.733128, best rearrangement setting 12
Bootstrap[17]: Time 0.064248 seconds, bootstrap likelihood -1845.866391, best rearrangement setting 12
Bootstrap[18]: Time 0.048456 seconds, bootstrap likelihood -1867.470969, best rearrangement setting 5
Bootstrap[19]: Time 0.046386 seconds, bootstrap likelihood -1850.905482, best rearrangement setting 8
Bootstrap[20]: Time 0.053808 seconds, bootstrap likelihood -1849.580119, best rearrangement setting 10
Bootstrap[21]: Time 0.051648 seconds, bootstrap likelihood -1743.551433, best rearrangement setting 6
Bootstrap[22]: Time 0.064499 seconds, bootstrap likelihood -1750.373724, best rearrangement setting 5
Bootstrap[23]: Time 0.062129 seconds, bootstrap likelihood -1723.976265, best rearrangement setting 7
Bootstrap[24]: Time 0.053066 seconds, bootstrap likelihood -1726.440640, best rearrangement setting 8
Bootstrap[25]: Time 0.046242 seconds, bootstrap likelihood -1551.978348, best rearrangement setting 6
Bootstrap[26]: Time 0.057425 seconds, bootstrap likelihood -1739.960620, best rearrangement setting 12
Bootstrap[27]: Time 0.061551 seconds, bootstrap likelihood -1705.071086, best rearrangement setting 10
Bootstrap[28]: Time 0.058037 seconds, bootstrap likelihood -1733.927772, best rearrangement setting 11
Bootstrap[29]: Time 0.052927 seconds, bootstrap likelihood -1864.138435, best rearrangement setting 12
Bootstrap[30]: Time 0.056051 seconds, bootstrap likelihood -1898.728446, best rearrangement setting 15
Bootstrap[31]: Time 0.054525 seconds, bootstrap likelihood -1753.862143, best rearrangement setting 15
Bootstrap[32]: Time 0.056043 seconds, bootstrap likelihood -1838.807043, best rearrangement setting 6
Bootstrap[33]: Time 0.052677 seconds, bootstrap likelihood -1819.940792, best rearrangement setting 15
Bootstrap[34]: Time 0.057016 seconds, bootstrap likelihood -1794.741546, best rearrangement setting 11
Bootstrap[35]: Time 0.054980 seconds, bootstrap likelihood -1728.002951, best rearrangement setting 8
Bootstrap[36]: Time 0.053418 seconds, bootstrap likelihood -1740.473518, best rearrangement setting 9
Bootstrap[37]: Time 0.066020 seconds, bootstrap likelihood -1937.437652, best rearrangement setting 11
Bootstrap[38]: Time 0.055222 seconds, bootstrap likelihood -1682.513674, best rearrangement setting 8
Bootstrap[39]: Time 0.056487 seconds, bootstrap likelihood -1798.823720, best rearrangement setting 13
Bootstrap[40]: Time 0.059086 seconds, bootstrap likelihood -1744.828721, best rearrangement setting 13
Bootstrap[41]: Time 0.065139 seconds, bootstrap likelihood -1682.294952, best rearrangement setting 10
Bootstrap[42]: Time 0.053573 seconds, bootstrap likelihood -1707.896274, best rearrangement setting 5
Bootstrap[43]: Time 0.067727 seconds, bootstrap likelihood -1835.447629, best rearrangement setting 14
Bootstrap[44]: Time 0.056112 seconds, bootstrap likelihood -1819.740290, best rearrangement setting 10
Bootstrap[45]: Time 0.053687 seconds, bootstrap likelihood -1818.575821, best rearrangement setting 15
Bootstrap[46]: Time 0.063936 seconds, bootstrap likelihood -1781.007635, best rearrangement setting 14
Bootstrap[47]: Time 0.055044 seconds, bootstrap likelihood -1835.010219, best rearrangement setting 8
Bootstrap[48]: Time 0.053713 seconds, bootstrap likelihood -1854.641665, best rearrangement setting 6
Bootstrap[49]: Time 0.055386 seconds, bootstrap likelihood -1674.070257, best rearrangement setting 7
Bootstrap[50]: Time 0.061729 seconds, bootstrap likelihood -1656.669756, best rearrangement setting 7
Bootstrap[51]: Time 0.065886 seconds, bootstrap likelihood -1820.272130, best rearrangement setting 11
Bootstrap[52]: Time 0.059192 seconds, bootstrap likelihood -1681.051701, best rearrangement setting 12
Bootstrap[53]: Time 0.054421 seconds, bootstrap likelihood -1596.706260, best rearrangement setting 8
Bootstrap[54]: Time 0.058151 seconds, bootstrap likelihood -1701.128340, best rearrangement setting 9
Bootstrap[55]: Time 0.052922 seconds, bootstrap likelihood -1981.314408, best rearrangement setting 11
Bootstrap[56]: Time 0.059652 seconds, bootstrap likelihood -1807.300073, best rearrangement setting 5
Bootstrap[57]: Time 0.067024 seconds, bootstrap likelihood -1795.879977, best rearrangement setting 7
Bootstrap[58]: Time 0.058072 seconds, bootstrap likelihood -1750.398954, best rearrangement setting 10
Bootstrap[59]: Time 0.056778 seconds, bootstrap likelihood -1535.167661, best rearrangement setting 9
Bootstrap[60]: Time 0.066582 seconds, bootstrap likelihood -1755.843381, best rearrangement setting 7
Bootstrap[61]: Time 0.065868 seconds, bootstrap likelihood -1597.030257, best rearrangement setting 5
Bootstrap[62]: Time 0.054720 seconds, bootstrap likelihood -1797.963028, best rearrangement setting 11
Bootstrap[63]: Time 0.055144 seconds, bootstrap likelihood -1953.006830, best rearrangement setting 12
Bootstrap[64]: Time 0.053467 seconds, bootstrap likelihood -1757.892813, best rearrangement setting 7
Bootstrap[65]: Time 0.054471 seconds, bootstrap likelihood -1760.615864, best rearrangement setting 5
Bootstrap[66]: Time 0.057662 seconds, bootstrap likelihood -1923.131069, best rearrangement setting 5
Bootstrap[67]: Time 0.061720 seconds, bootstrap likelihood -1718.388512, best rearrangement setting 15
Bootstrap[68]: Time 0.058659 seconds, bootstrap likelihood -1959.962535, best rearrangement setting 11
Bootstrap[69]: Time 0.066413 seconds, bootstrap likelihood -1855.457975, best rearrangement setting 5
Bootstrap[70]: Time 0.066409 seconds, bootstrap likelihood -1877.114129, best rearrangement setting 8
Bootstrap[71]: Time 0.056567 seconds, bootstrap likelihood -1744.424843, best rearrangement setting 10
Bootstrap[72]: Time 0.058611 seconds, bootstrap likelihood -1873.743983, best rearrangement setting 11
Bootstrap[73]: Time 0.055472 seconds, bootstrap likelihood -1555.648313, best rearrangement setting 9
Bootstrap[74]: Time 0.056715 seconds, bootstrap likelihood -1681.963093, best rearrangement setting 5
Bootstrap[75]: Time 0.048767 seconds, bootstrap likelihood -1872.808120, best rearrangement setting 8
Bootstrap[76]: Time 0.054894 seconds, bootstrap likelihood -1832.071225, best rearrangement setting 9
Bootstrap[77]: Time 0.051213 seconds, bootstrap likelihood -1900.187287, best rearrangement setting 11
Bootstrap[78]: Time 0.063422 seconds, bootstrap likelihood -1856.651511, best rearrangement setting 15
Bootstrap[79]: Time 0.053028 seconds, bootstrap likelihood -1651.349141, best rearrangement setting 9
Bootstrap[80]: Time 0.056216 seconds, bootstrap likelihood -1800.035227, best rearrangement setting 15
Bootstrap[81]: Time 0.052663 seconds, bootstrap likelihood -1679.915077, best rearrangement setting 7
Bootstrap[82]: Time 0.051474 seconds, bootstrap likelihood -1703.979494, best rearrangement setting 6
Bootstrap[83]: Time 0.056506 seconds, bootstrap likelihood -1690.533242, best rearrangement setting 10
Bootstrap[84]: Time 0.063764 seconds, bootstrap likelihood -1709.046610, best rearrangement setting 11
Bootstrap[85]: Time 0.058011 seconds, bootstrap likelihood -1780.174967, best rearrangement setting 8
Bootstrap[86]: Time 0.066347 seconds, bootstrap likelihood -1685.333323, best rearrangement setting 7
Bootstrap[87]: Time 0.054518 seconds, bootstrap likelihood -1719.553400, best rearrangement setting 7
Bootstrap[88]: Time 0.066142 seconds, bootstrap likelihood -1861.799524, best rearrangement setting 12
Bootstrap[89]: Time 0.065435 seconds, bootstrap likelihood -1577.118525, best rearrangement setting 10
Bootstrap[90]: Time 0.054877 seconds, bootstrap likelihood -1877.840110, best rearrangement setting 8
Bootstrap[91]: Time 0.056633 seconds, bootstrap likelihood -1872.711391, best rearrangement setting 12
Bootstrap[92]: Time 0.056456 seconds, bootstrap likelihood -1818.747280, best rearrangement setting 13
Bootstrap[93]: Time 0.057307 seconds, bootstrap likelihood -1708.171311, best rearrangement setting 15
Bootstrap[94]: Time 0.054421 seconds, bootstrap likelihood -1686.483935, best rearrangement setting 5
Bootstrap[95]: Time 0.049227 seconds, bootstrap likelihood -1731.159425, best rearrangement setting 5
Bootstrap[96]: Time 0.049824 seconds, bootstrap likelihood -1663.620895, best rearrangement setting 13
Bootstrap[97]: Time 0.063568 seconds, bootstrap likelihood -1954.461883, best rearrangement setting 11
Bootstrap[98]: Time 0.053750 seconds, bootstrap likelihood -1757.724224, best rearrangement setting 6
Bootstrap[99]: Time 0.056846 seconds, bootstrap likelihood -1676.000406, best rearrangement setting 14


Overall Time for 100 Rapid Bootstraps 6.172358 seconds
Average Time per Rapid Bootstrap 0.061724 seconds

Starting ML Search ...

Fast ML optimization finished

Fast ML search Time: 4.416666 seconds

Slow ML Search 0 Likelihood: -1799.554165
Slow ML Search 1 Likelihood: -1799.554165
Slow ML Search 2 Likelihood: -1799.554165
Slow ML Search 3 Likelihood: -1799.554178
Slow ML Search 4 Likelihood: -1799.554178
Slow ML Search 5 Likelihood: -1799.554178
Slow ML Search 6 Likelihood: -1799.554178
Slow ML Search 7 Likelihood: -1799.554178
Slow ML Search 8 Likelihood: -1799.554178
Slow ML Search 9 Likelihood: -1799.554179
Slow ML optimization finished

Slow ML search Time: 1.280160 seconds
Thorough ML search Time: 0.129046 seconds

Final ML Optimization Likelihood: -1799.560107

Model Information:

Model Parameters of Partition 0, Name: No Name Provided, Type of Data: DNA
alpha: 0.265629
Tree-Length: 2.172749
rate A <-> C: 0.970478
rate A <-> G: 2.225205
rate A <-> T: 0.916084
rate C <-> G: 0.075735
rate C <-> T: 2.872117
rate G <-> T: 1.000000

freq pi(A): 0.272569
freq pi(C): 0.205966
freq pi(G): 0.213699
freq pi(T): 0.307765


ML search took 5.826319 secs or 0.001618 hours

Combined Bootstrap and ML search took 11.998707 secs or 0.003333 hours

Drawing Bootstrap Support Values on best-scoring ML tree ...



Found 1 tree in File /home/.public/RAxML_bestTree.out_codon



Found 1 tree in File /home/.public/RAxML_bestTree.out_codon

Program execution info written to /home/.public/RAxML_info.out_codon
All 100 bootstrapped trees written to: /home/.public/RAxML_bootstrap.out_codon

Best-scoring ML tree written to: /home/.public/RAxML_bestTree.out_codon

Best-scoring ML tree with support values written to: /home/.public/RAxML_bipartitions.out_codon

Best-scoring ML tree with support values as branch labels written to: /home/.public/RAxML_bipartitionsBranchLabels.out_codon

Overall execution time for full ML analysis: 12.001175 secs or 0.003334 hours or 0.000139 days