MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0002277MEGADocumentationpublic2020-10-08 10:472023-04-14 18:39
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformMacOSOS XOS Versionother
Product VersionMEGA-CC 11 (command line version) 
Target VersionFixed in Version 
First NameNicoletta
Last NameCommins
Emailnacommins@g.harvard.edu
Confirm Emailnacommins@g.harvard.edu
Summary0002277: Specify multiple taxa as an outgroup
DescriptionSorry I reported a short description yesterday but I have some clarification. I am trying to run a ML molecular clock test and I can't figure out how to specify an outgroup clade in MEGA-CC. I can't find this anywhere in any of the documentation or examples.
Steps To ReproduceMy command has the following structure:

megacc -a my_file.mao -d my_alignment_file.fasta -t my_tree.nwk -g outgroup_file.txt -o output_prefix

I can get it to run when my outgroups file looks like this:

SAMEA2071449=outgroup

However, when I tried:

SAMEA2071449,SAMEA2275848,SAMEA2259646,SAMN09758979=outgroup

I got the following error:

SAMEA2071449,SAMEA2275848,SAMEA2259646,SAMN09758979=outgroup

I also tried a file with the format:

SAMEA2071449=outgroup
SAMEA2275848=outgroup
SAMEA2259646=outgroup
SAMN09758979=outgroup

And got the following error:

Error: Reltime analysis failed: Error when computing node heights: Access violation

For all three attempts I used the exact same command with the exception of the groups file with the exact same request for amount of memory, etc.
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Issue History
Date ModifiedUsernameFieldChange
2020-10-08 10:47guestNew Issue
2022-03-08 07:21guestNote Added: 0004951
2022-12-05 06:48guestNote Added: 0005828
2023-04-14 18:39guestNote Added: 0006511

Notes
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