0003631: Phylogeneic tree calculation exits without warning - MantisBT

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Project

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Date Submitted

Last Update

0003631

MEGA

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public

2022-04-25 14:02

2023-04-14 18:53

Reporter

guest

Assigned To

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

new

Resolution

open

Platform

PC

OS

Linux

Product Version

MEGA 11 (Graphical Interface version)

Target Version

Fixed in Version

Summary

0003631: Phylogeneic tree calculation exits without warning

Description

Version 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 Reproduce

Pylogeny>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

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First Name

Mark

Last Name

Lindstrom

Email

electronorbit@protonmail.com

Confirm Email

electronorbit@protonmail.com

Kivu sequence _public isolates_selected_21_08.mas (278,360 bytes) 1969-12-31 17:33

Relationships

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 (reporter) 2023-04-14 18:53	https://www.estoolcarbide.com/product/cnmg-pressing-cermet-inserts-p-1193/ [^] [CNMG Cermet Inserts] http://laborers.blog.jp/ [^] [http://laborers.blog.jp/ [^]] https://vanherman.exblog.jp/ [^] [special inserts] https://billkyle.exblog.jp/ [^] [central and intermediate inserts] https://jeromelind.exblog.jp/ [^] [tungsten carbide tubes] https://scottthere.exblog.jp/ [^] [carbide rod stock] http://easytouse.blog.jp/ [^] [http://easytouse.blog.jp/ [^]] https://jacobupton.exblog.jp/ [^] [threading insert] http://wideworld.blog.jp/ [^] [http://wideworld.blog.jp/ [^]]

Issue History
Date Modified	Username	Field	Change
1969-12-31 17:33	user19	Status	new => assigned
1969-12-31 17:33	user19	Assigned To	=> user19
1969-12-31 17:33	user19	Note Added: 0002420
1969-12-31 17:33	user614	Tag Attached: session_files
2022-04-25 14:02	guest	New Issue
2023-04-14 18:53	guest	Note Added: 0006686

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