MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0000585MEGACaption Expertpublic2017-11-01 00:282017-11-07 09:16
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionfixed 
PlatformPCOSWindowsOS Version10
Product VersionMEGA 11 (Graphical Interface version) 
Target VersionFixed in Version 
First NameAlmero
Last NameOosthuizen
Emailalmero@nzg.ac.za
Confirm Emailalmero@nzg.ac.za
Summary0000585: Best-fit model select suggests values not allowed when constructing phylogenetic trees
DescriptionBest-fit substitution model suggests +I and +G values that cannot be entered under the "No of discrete gamma catagories" section during maximum-likelihood tree construction. Error message is "1.09 is not a valid integer value".
Steps To ReproduceRun Best-fit substitution model on data, +G values below 2 cause this error.
Click phylogeny, select "construct/test ML tree".
Set parameters - Test of phylogeny = bootstrap
replicates = 1000
substitution type = nucleotide
model/method = any
rates among sites = gamma

gaps/missing data = use all sites (data was trimmed to shortest sequence +-530bp).
all codon positions selected
ML Heuristic method = NNI
Initial tree for ML = automatic (default NJ/BioNJ)
Branch swap filter = Moderate
No of discrete gamma categories = 1.09
Initially entering gamma = 1.09 last and pressing enter allows the run to proceed. Trying to edit this value later for a different analysis results in error message.
Additional Information
TagsNo tags attached.
Relationships
Attached Filespng MEGA7 error.png (96,635) 2017-11-01 00:28
https://megasoftware.net/mantis_bt/
Issue History
Date ModifiedUsernameFieldChange
2017-11-01 00:28guestNew Issue
2017-11-01 00:28guestFile Added: MEGA7 error.png
2017-11-07 09:16gstecherNote Added: 0003881
2017-11-07 09:16gstecherStatusnew => resolved
2017-11-07 09:16gstecherResolutionopen => fixed
2017-11-07 09:16gstecherAssigned To => gstecher

Notes
(0000481)
paul   
1969-12-31 17:33   
Suggestion is saved. Sent thank you email to user. This suggestion is closed.
(0003881)
gstecher   
2017-11-07 09:16   
Hi Almero,

I am writing in response to the bug report you recently submitted regarding the MEGA software. To resolve the error you can do the following:

    Close MEGA if it is opened
    Navigate to the AppData directory by entering %appdata% in the Windows Explorer address bar and pressing enter
    This will open the c:\users\username\AppData\Roaming directory. Once in that directory, delete the folder MEGA7_7170509-x86_64
    Open MEGA and run the analysis

On a side note, Gamma Parameter and No of Discrete Gamma Categories are completely unrelated, so you should not enter 1.09 for No of Discrete Categories (it should be an integer value, such as 5).

--
Best regards,

Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu