MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0003631MEGA[All Projects] Feedbackpublic2022-04-25 14:022023-04-14 18:53
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformPCOSLinuxOS Versionother
Product VersionMEGA 11 (Graphical Interface version) 
Target VersionFixed in Version 
First NameMark
Last NameLindstrom
Emailelectronorbit@protonmail.com
Confirm Emailelectronorbit@protonmail.com
Summary0003631: Phylogeneic tree calculation exits without warning
DescriptionVersion 11.0.11 running on Ubunu 20.04 (same issue with previous verion of MEGA I used which was downloaded 6 mo to 12 mo ago but cant recall version)
At some stage when calculating (In above sometime after boostrap number 0000173:0000180 calculation), the program exited without warning. This happens >80% of the time when using the software and to get it to work I need to reduce the number of boostraps, usually to c. 100 to get app to finish.
With smaller datasets I have found that increasing number of threads fixes the exit without warning, but not in this case. Note several genomes have sections of missing sequences and N's are used.
This crash happens both with full length (30,000 nt) and short sequences (eg 500nt)
All seqs aligned with MUSCLE prior to use in MEGA
Steps To ReproducePylogeny>Construct/Test ML Tree
(fastas file is 1MB), nucleotide seqs
Stat method: ML
Test:Bootstrap
No. Bootstrp reps:1000
Sub tyle:nt
Model:GTR
Use all sites
Codon pos: all
ML heuristic model:NNI
Initial tree for ML:Default
No. threads:34
Additional Information
TagsNo tags attached.
Relationships
Attached Files? Kivu sequence _public isolates_selected_21_08.mas (278,360) 1969-12-31 17:33
https://megasoftware.net/mantis_bt/
Issue History
Date ModifiedUsernameFieldChange
1969-12-31 17:33user19Statusnew => assigned
1969-12-31 17:33user19Assigned To => user19
1969-12-31 17:33user19Note Added: 0002420
1969-12-31 17:33user614Tag Attached: session_files
2022-04-25 14:02guestNew Issue
2023-04-14 18:53guestNote Added: 0006686

Notes
(0002420)
user19   
1969-12-31 17:33   
Dear Helmut,

When you use a corrupted alignment explorer session file all sorts of things can go wrong. The Alignment session (mts) contains information about how your view was setup, including such things a font size, color, item names, options checked, etc. If a corrupted file is used you may end up with a very strange display, and possibly corrupted sequences. You may want to re-download the file. As long as you don’t use broken files everything works fine.

I hope that answered your concern.

Daniel Peterson
Center for Evolutionary Medicine and Informatics
The Biodesign Institute at Arizona State University
(0006686)
guest   
2023-04-14 18:53   
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