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| ID | Project | Category | View Status | Date Submitted | Last Update | ||||
| 0000095 | MEGA | [All Projects] Feedback | public | 2016-03-16 06:39 | 2016-03-16 12:05 | ||||
| Reporter | guest | ||||||||
| Assigned To | gstecher | ||||||||
| Priority | normal | Severity | minor | Reproducibility | have not tried | ||||
| Status | resolved | Resolution | no change required | ||||||
| Platform | OS | ||||||||
| Product Version | MEGA 11 (Graphical Interface version) | ||||||||
| Target Version | Fixed in Version | ||||||||
| Summary | 0000095: Optimizing system performance | ||||||||
| Description | I have a student that is needing to increase the speed of the program. We estimate with a standard desktop, it will take another 30 days. I have downloaded the MEGA software onto an Amazon Web Services machine with 160 GB of memory. However, the system doesn't seem to be taking advantage of the extra memory and computational speed. Do you find this to be the case that the algorithms in MEGA will not utilize the machines memory when available? | ||||||||
| Tags | No tags attached. | ||||||||
| Attach Tags | (Separate by ",") | ||||||||
| First Name | John | ||||||||
| Last Name | Crooker | ||||||||
| crooker@ucmo.edu | |||||||||
| Confirm Email | crooker@ucmo.edu | ||||||||
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(0003636) gstecher (administrator) 2016-03-16 11:24 |
Hi John, I am writing in response to your question regarding the MEGA software. Can you describe what it is your student is doing? Which version of MEGA is being used? Which analyses, settings, etc...? What are the characteristics of the data being used? -- Best regards, Glen Stecher |
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(0003637) gstecher (administrator) 2016-03-16 12:05 |
Hi Skip, Thanks for the info. The student is using the ClustalW algorithm which is much slower than the other option in MEGA which is the MUSCLE algorithm. I would ask the student to use the MUSCLE algorithm and set MaxIters to 2 in the options dialog. If that is still too slow, the student can check out MAFFT (http://mafft.cbrc.jp/alignment/software/ [^]). On 03/16/2016 11:33 AM, Skip Crooker wrote: > Hi Glen, > > We are using MEGA 7.0.14(7160202-x86_64). We have sequences in a .mas file. We are aligning the sequences. Attached is an image listing the resource usage on a computer with 160GB of RAM. I'm a computer person and not familiar with the goal of the analysis. I can ask the student and her Faculty advisor to provide more insights on the exact application. > > In terms of the system performance, you can see the software is only using about 2% of the available memory and 3% of the computational processor speed. We estimate with just a standard desktop the alignment will take 40 days. So, I'm trying to find a way to speed this up with this more powerful computer system. > > Skip |
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Issue History |
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| Date Modified | Username | Field | Change |
| 2016-03-16 06:39 | guest | New Issue | |
| 2016-03-16 11:24 | gstecher | Assigned To | => gstecher |
| 2016-03-16 11:24 | gstecher | Status | new => assigned |
| 2016-03-16 11:24 | gstecher | Note Deleted: 0000010 | |
| 2016-03-16 11:24 | gstecher | Note Added: 0003636 | |
| 2016-03-16 11:24 | gstecher | File Deleted: phylip1_alignment5.txt | |
| 2016-03-16 12:05 | gstecher | Note Added: 0003637 | |
| 2016-03-16 12:05 | gstecher | Status | assigned => resolved |
| 2016-03-16 12:05 | gstecher | Resolution | open => no change required |
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Issue History |
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