MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0001822MEGAAlignment Explorerpublic2020-03-05 10:032020-03-09 09:15
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionno change required 
PlatformMacOSOS XOS Version10.11
Product Version 
Target VersionFixed in Version 
First NameBaozhong
Last NameMeng
Emailbmeng@uoguelph.ca
Confirm Emailbmeng@uoguelph.ca
Summary0001822: Error sign_Invalid base found: \ in line 6
DescriptionWhen I complete an MSA using the ClustalW within MEGAX, and import the aligned data to run phylogeny using any of the methods, it always give me an error warning Invalid base found: \ in line xx. Can you please let me know how to resolve this issue?

Thank you for the help,

Baozhong Meng
Associate Professor
University of Guelph
Ontario, Canada
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Issue History
Date ModifiedUsernameFieldChange
1969-12-31 17:33user19Statusnew => assigned
1969-12-31 17:33user19Assigned To => agasky
1969-12-31 17:33agaskyNote Added: 0001592
1969-12-31 17:33agaskyStatusassigned => resolved
1969-12-31 17:33agaskyResolutionopen => fixed
2020-03-05 10:03guestNew Issue
2020-03-09 09:15gstecherNote Added: 0004419
2020-03-09 09:15gstecherStatusnew => resolved
2020-03-09 09:15gstecherResolutionopen => no change required
2020-03-09 09:15gstecherAssigned To => gstecher

Notes
(0001592)
agasky   
1969-12-31 17:33   
Sent user updated snippet from MEGA5's help file which has is correct.
(0004419)
gstecher   
2020-03-09 09:15   
Hi Baozhong,


The error is not in MEGA but in the data file. It is not a FASTA formatted file. I have no idea what format it is but no version of MEGA can work with it as parsing it leads to backslash characters in the sequence data. If you open the file in a text editor you will see.


On 3/7/2020 11:03 AM, Baozhong Meng wrote:
> Hi Glen,
>
> Thanks for getting back to me and your willing to help. I believe I have already discarded the meg file since it did not work after several attempts but will check this out when I go to my office on Monday.
>
> I attach the .fasta file for you here so that you can start from the MSA, if you would like to. It will take quite while to complete the alignment since the data set is quite large (at least on my own computer). It contains 65 genomes of coronaviruses from bats, each nearly 30 kb in length.
>
> Please let me know what you will find out.