

IMPORTANT WARNING: Sequences 1053439 and 1005430 are exactly identical


IMPORTANT WARNING: Sequences 930322 and 4363202 are exactly identical


IMPORTANT WARNING: Sequences 835100 and 194205 are exactly identical


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IMPORTANT WARNING: Sequences 4341349 and 4481373 are exactly identical


IMPORTANT WARNING: Sequences 4383405 and 4407478 are exactly identical


IMPORTANT WARNING: Sequences 4449794 and 4475831 are exactly identical

IMPORTANT WARNING
Found 139 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.

An alignment file with sequence duplicates removed has already
been printed to file gg_13_5_ssu_align_99_pfiltered.fasta.reduced


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



This is RAxML version 8.1.24 released by Alexandros Stamatakis on June 29 2015.

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

Alignment has 1285 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 4.51%

RAxML rapid hill-climbing mode

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


Executing 1 inferences on the original alignment using 1 user-specified trees

All free model parameters will be estimated by RAxML
ML estimate of 25 per site rate categories

Likelihood of final tree will be evaluated and optimized under GAMMA

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

Partition: 0
Alignment Patterns: 1285
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR




RAxML was called as follows:

raxmlHPC-PTHREADS -s gg_13_5_ssu_align_99_pfiltered.fasta -m GTRCAT -n score-f -F -g 99_otus_nice.tree -T 16 -p 32323 


Base frequencies: 0.250954 0.234726 0.318990 0.195330 

Inference[0]: Time 20468.479701 CAT-based likelihood -20826993.474014, best rearrangement setting 5
alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 0.947786 2.643649 1.480482 0.786790 4.471837 1.000000


NOT conducting any final model optimizations on all 1 trees under CAT-based model ....

Final GAMMA  likelihood: -20884160.339468

REMEMBER that CAT-based likelihood scores are meaningless!

Program execution info written to /oasis/projects/nsf/uot136/smirarab/EMP/RAxML_info.score-f
Overall execution time: 20969.915871 secs or 5.824977 hours or 0.242707 days

