MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0000620MEGACalculation Errorpublic2017-12-07 12:102017-12-07 12:10
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformMacOSOS XOS Version10.10
Product VersionMEGA-CC 11 (command line version) 
Target VersionFixed in Version 
First NameKecen
Last NameZhou
Emailkecen.zhou@live.com
Confirm Emailkecen.zhou@live.com
Summary0000620: Selenocysteine not a valid base?
DescriptionHello,

I am trying to make a protein tree using Mega-CC.

I used the command
Kecen$ megacc -a /Users/Kecen/Documents/megacc/infer_NJ_protein.mao -d /Users/Kecen/Documents/M7CC_Out/prottreegenes-4646.meg

And was told
Data file = /Users/Kecen/Documents/M7CC_Out/prottreegenes-4646.meg
  AnalysisFile = /Users/Kecen/Documents/megacc/infer_NJ_protein.mao
  Message = Invalid base found: U (in line 969)

U is obviously a valid base, so what went wrong here?
Steps To ReproduceMake alignment using a FASTA with sequences with U in them.
Pairwise Alignment : ====================
                          : ProteinPWGapOpeningPenalty : 10.00
                          : ProteinPWGapExtensionPenalty : 0.20
                          : Multiple Alignment : ====================
                          : ProteinMAGapOpeningPenalty : 10.00
                          : ProteinMAGapExtensionPenalty : 0.20
                          : Global Options : ====================
                          : ProteinWeightMatrix : BLOSUM
                          : Residue-specificPenalties : ON
                          : HydrophillicPenalties : ON
                          : GapSeperationDistance : 4
                          : EndGapSeperation : OFF
                          : UseNegativeMatrix : OFF
                          : DelayDivergentCutoff : 30
                          : KeepPredefinedGaps : True
                          : datatype : snProtein
                          : missingBaseSymbol : ?
                          : identicalBaseSymbol : .
                          : gapSymbol : -

Make a Neighbor Joining tree using the Poisson model, 80% partial deletion, gamma 1.0 in the .mao files.
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Attached Fileszip testfiles.zip (34,223) 2017-12-07 12:10
https://megasoftware.net/mantis_bt/
Issue History
Date ModifiedUsernameFieldChange
2017-12-07 12:10guestNew Issue
2017-12-07 12:10guestFile Added: testfiles.zip

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