0000139: RAM Allocation Issue

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0000139

MEGA

Alignment Explorer

public

2016-04-29 12:37

2016-05-05 07:23

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

resolved

Resolution

won't fix

Platform

Windows

Product Version

MEGA 11 (Graphical Interface version)

Target Version

Fixed in Version

Summary

0000139: RAM Allocation Issue

Description

I'm attempting to align a DNA sequence using the Muscle application in MEGA 7. The fasta file I'm working with is 5.8 GB, and contains mitochondrial sequence information for around 2600 subjects. In the "Align node" part of the alignment process, it works fine until it reaches around 57% of the first iteration, or around 2 GB of memory being used. Once it hits this point, it stops completely and gives me an error that says my computer is reporting a lack of enough RAM. This machine has 24 GB of RAM, and it seems like the MEGA software is putting a cap on how much RAM it can use. I know this was the case in MEGA6, but in MEGA7 it has been improved to use the maximum amount of RAM it can. We tried changing the value in the "Max Memory in MB" field to an unreasonably high number, but this did not help. We have tried this on other computers as well, including a Mac and a PC that has worse specs than the original machine. Is there a way to allow MEGA to use all of the available RAM of the computer?

Steps To Reproduce

Attempt to align a large Fasta file (around 5.8 GB) using Muscle, and make note of the "Memory Used (MB)" progress in the "Run Status" window. Once it gets to around 2000 MB (2 GB), the program crashes and says the computer does not have enough RAM.

Additional Information

We tried splitting the sequence in half to see if the file size could have had something to do with it, and we were able to successfully align it as long as we made sure the computer was using no more than 2 GB of memory in the process. This does not solve our problem, however, as we need to align this much larger fasta file in order to make a good phylogenetic tree downstream.

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First Name

Corey

Last Name

Liebowitz

cliebo@gmail.com

Confirm Email

cliebo@gmail.com

Attached Files

out.zip (128,136 bytes) 1969-12-31 17:33

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Notes
(0000029) gstecher (administrator) 1969-12-31 17:33	I found that a combination of concatenation and a TStringList was slowing me down so I cleaned up the concatenation and replaced the TStringList with a THashedStringList;

(0003657) gstecher (administrator) 2016-05-05 07:23	Hi Corey, I am writing in response to your question regarding MUSCLE sequence alignment in MEGA. MEGA does not implement the MUSCLE algorithm but rather it launches the MUSCLE executable program in a separate process. Unfortunately, the author of MUSCLE does not distribute a 64-bit executable for Windows and so it can only allocate ~2GB of memory on Windows systems. If you have access to a 64-bit Linux or Mac system, then you can download the MUSCLE executable for either of those platforms and use that to perform sequence alignment. Otherwise, you may wish to use MAFFT or some other alignment software. -- Best regards, Glen Stecher Institute for Genomics and Evolutionary Medicine igem.temple.edu

Issue History
Date Modified	Username	Field	Change
2016-04-29 12:37	guest	New Issue
2016-05-05 07:23	gstecher	Note Added: 0003657
2016-05-05 07:23	gstecher	Status	new => resolved
2016-05-05 07:23	gstecher	Resolution	open => won't fix
2016-05-05 07:23	gstecher	Assigned To	=> gstecher