MantisBT - MEGA |
| View Issue Details |
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| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0000363 | MEGA | Main Form | public | 2017-01-13 11:34 | 2017-01-27 13:21 |
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| Reporter | guest | |
| Assigned To | gstecher | |
| Priority | normal | Severity | minor | Reproducibility | have not tried |
| Status | resolved | Resolution | no change required | |
| Platform | PC | OS | Windows | OS Version | 10 |
| Product Version | MEGA 11 (Graphical Interface version) | |
| Target Version | | Fixed in Version | | |
| First Name | Nick |
| Last Name | Waters |
| Email | nickdwaters@gmail.com |
| Confirm Email | nickdwaters@gmail.com |
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| Summary | 0000363: Memory leak during ML phylogenetic analysis |
| Description | Windows 10 x64 (8 gb RAM) wants to shut MEGA down due to lack of memory about halfway through ML phylogenetic analysis. I increased pagefile to 32 gb and it still ran out of physical and pagefile virtual memory, completing only 109 of 250 bootstraps. Note: Closing the analysis windows such that MEGA GUI is all that is running still does not release memory! Once you exit MEGA then memory is released. This problem only occurs when selecting Construct/Test Maximum-likelihood tree. The other tree building methods do not cause the problem. Memory is also not released when aborting tree building.
The analysis uses 56 sequences with 1142 nucleotides.
Evolutionary model does not matter.
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| Steps To Reproduce | Problem only occurs during Construct/Test Maximum-likelihood tree. All models exhibit the problem. The only setting which appears to allow construction to finish is to mitigate the problem by reducing SPR from 5 to 3, and setting Branch Swap Filter to weak. However, even when the tree is finished, memory is still not released. If you Stop analysis, memory is not released.
Analysis
Analysis ------------------------ Phylogeny Reconstruction
Statistical Method -------------- Maximum Likelihood
Phylogeny Test
Test of Phylogeny --------------- Bootstrap method
No. of Bootstrap Replications --- 250
Substitution Model
Substitutions Type -------------- Nucleotide
Model/Method -------------------- Tamura-Nei model
Rates and Patterns
Rates among Sites --------------- Gamma Distributed (G)
No of Discrete Gamma Categories - 16
Data Subset to Use
Gaps/Missing Data Treatment ----- Complete deletion
Tree Inference Options
ML Heuristic Method ------------- Subtree-Pruning-Regrafting - Extensive (SPR level 5)
Initial Tree for ML ------------- Make initial tree automatically (Default - NJ/BioNJ)
Branch Swap Filter -------------- None
System Resource Usage
Number of Threads --------------- 4
Codons Included ------------------- 1st+2nd+3rd+Non-Coding
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| Additional Information | I've attached the sequence data for you to explore. I've enjoyed using MEGA for several years. Hope the problem is resolved soon. |
| Tags | No tags attached. |
| Relationships | |
| Attached Files |  cytb_cleaned_aligned_with_Nielsen_and_outgroups_trimmed reduced ASMO v4.mas (66,396) 2017-01-13 11:34
https://megasoftware.net/mantis_bt/ |
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| Issue History |
| Date Modified | Username | Field | Change |
| 2017-01-13 11:34 | guest | New Issue | |
| 2017-01-13 11:34 | guest | File Added: cytb_cleaned_aligned_with_Nielsen_and_outgroups_trimmed reduced ASMO v4.mas | |
| 2017-01-27 13:21 | gstecher | Note Added: 0003749 | |
| 2017-01-27 13:21 | gstecher | Status | new => resolved |
| 2017-01-27 13:21 | gstecher | Resolution | open => no change required |
| 2017-01-27 13:21 | gstecher | Assigned To | => gstecher |