0006599: Sequence Alignment SLOW, Not using Processing Power

MantisBT - MEGA
View Issue Details

ID	Project	Category	View Status	Date Submitted	Last Update
0006599	MEGA	Alignment Explorer	public	2024-06-20 19:33	2024-06-20 19:33

Reporter	guest
Assigned To
Priority	normal	Severity	minor	Reproducibility	have not tried
Status	new	Resolution	open
Platform	PC	OS	Windows	OS Version	10
Product Version	MEGA 11 (Graphical Interface version)
Target Version		Fixed in Version
First Name	Joel
Last Name	Goldberg
Email	jbg001@lsuhs.edu
Confirm Email	jbg001@lsuhs.edu

Summary	0006599: Sequence Alignment SLOW, Not using Processing Power
Description	After trying to run the ClustalW nucleotide sequence alignment on my MacBook for 50 hours and getting nowhere (bad idea), I tried to run it on my desktop with AMD Ryzen 7 3700X 8-core processor and 48 gigs of DDR4-3600 ram. To my surprise, the software fails to utilize available resources, never surpassing 10% processor load on 2 cores/4 threads total and never drawing more than 1.5 gb of ram usage. I am unable to locate settings to expand available draw or usage to perform the sequence alignment for Clustal, but I did locate an option to set max memory usage for Muscle alignment. However, every time I run Muscle alignment, it fails due to being "unable to open" the muscle file it creates in the first step of the alignment run.
Steps To Reproduce	Load FASTA files for both mutant and wild type Bordetella bronchiseptica RB50 genomes (5.339 Megabases each). Run ClustalW or Muscle nucleotide sequence alignment.
Additional Information
Tags	No tags attached.
Relationships
Attached Files	Screenshot 2024-06-20 213234.png (131,470) 2024-06-20 19:33 https://megasoftware.net/mantis_bt/

Issue History
Date Modified	Username	Field	Change
2024-06-20 19:33	guest	New Issue
2024-06-20 19:33	guest	File Added: Screenshot 2024-06-20 213234.png

There are no notes attached to this issue.