MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0004367MEGA[All Projects] Feedbackpublic2023-01-12 14:172023-04-14 00:50
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformOSOS Version
Product VersionMEGA-CC 11 (command line version) 
Target VersionFixed in Version 
First NameZach
Last NameMalloy
Emailmalloyza@oregonstate.edu
Confirm Emailmalloyza@oregonstate.edu
Summary0004367: Application Error
DescriptionI keep getting the error "Application Error finalizing MUSCLE alignment: unable to open file.
How do I resolve this issue?
Steps To Reproduce
Additional Information
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Attached Files? tree march 2013.phy (157,810) 1969-12-31 17:33
https://megasoftware.net/mantis_bt/
Issue History
Date ModifiedUsernameFieldChange
1969-12-31 17:33user19Note Added: 0003057
1969-12-31 17:33user19Statusnew => resolved
1969-12-31 17:33user19Resolutionopen => fixed
1969-12-31 17:33user19Assigned To => user19
1969-12-31 17:33user19Note Added: 0003058
2023-01-12 14:17guestNew Issue
2023-04-14 00:50guestNote Added: 0006319

Notes
(0003057)
user19   
1969-12-31 17:33   
The file included spaces in the sequence name. Since there's multiple phylip formats (inf length names delimited by 'space' and there's the max 10 char name) we attempt to pick the right format, but the space in the middle of the name confused MEGA.
(0003058)
user19   
1969-12-31 17:33   
Hi Heidi,

I took a look at the file you sent me. The problem is that the sequence names contain spaces. Since there’s so many different implementations of the phylip format, MEGA tries it’s best to convert all of them properly. This means there’s somewhat complicated logic which has to decide whether a name is of the 10 character format, or is some other length and terminates with a space. Anyway, just remove the spaces in the names and the file should convert just fine.

Daniel Peterson
(0006319)
guest   
2023-04-14 00:50   
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