MantisBT - MEGA |
| View Issue Details |
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| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0000139 | MEGA | Alignment Explorer | public | 2016-04-29 12:37 | 2016-05-05 07:23 |
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| Reporter | guest | |
| Assigned To | gstecher | |
| Priority | normal | Severity | minor | Reproducibility | have not tried |
| Status | resolved | Resolution | won't fix | |
| Platform | PC | OS | Windows | OS Version | 7 |
| Product Version | MEGA 11 (Graphical Interface version) | |
| Target Version | | Fixed in Version | | |
| First Name | Corey |
| Last Name | Liebowitz |
| Email | cliebo@gmail.com |
| Confirm Email | cliebo@gmail.com |
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| 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. |
| Tags | No tags attached. |
| Relationships | |
| Attached Files |  out.zip (128,136) 1969-12-31 17:33
https://megasoftware.net/mantis_bt/ |
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| 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 |