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| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0006599 | MEGA | Alignment Explorer | public | 2024-06-20 19:33 | 2024-06-20 19:33 |
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| Reporter | guest | |
| Assigned To | | |
| Priority | normal | Severity | minor | Reproducibility | have not tried |
| Status | new | Resolution | open | |
| Platform | PC | OS | Windows | |
| Product Version | MEGA 11 (Graphical Interface version) | |
| Target Version | | Fixed in Version | | |
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| 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. |
| Tags | No tags attached. |
| Attach Tags | (Separate by ",")
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| First Name | Joel |
| Last Name | Goldberg |
| Email | jbg001@lsuhs.edu |
| Confirm Email | jbg001@lsuhs.edu |
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| Attached Files |  Screenshot 2024-06-20 213234.png (131,470 bytes) 2024-06-20 19:33 |
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