0000620: Selenocysteine not a valid base? - MantisBT

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ID

Project

Category

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Date Submitted

Last Update

0000620

MEGA

Calculation Error

public

2017-12-07 12:10

2017-12-07 12:10

Reporter

guest

Assigned To

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

new

Resolution

open

Platform

Mac

OS

OS X

Product Version

MEGA-CC 11 (command line version)

Target Version

Fixed in Version

Summary

0000620: Selenocysteine not a valid base?

Description

Hello,

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 Reproduce

Make 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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First Name

Kecen

Last Name

Zhou

Email

kecen.zhou@live.com

Confirm Email

kecen.zhou@live.com

testfiles.zip (34,223 bytes) 2017-12-07 12:10

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Issue History
Date Modified	Username	Field	Change
2017-12-07 12:10	guest	New Issue
2017-12-07 12:10	guest	File Added: testfiles.zip

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