Hi Susan, On Thu, 2015-11-19 at 20:52 +0000, Susan Beth Fogelson wrote: > I am using Mauve to align approximately 35 bacterial genomes to a > reference. Currently I am using a desktop computer with 16GB of RAM. > I started the alignment about 2 days ago and it is still running, is > this a normal time frame? Is there a way I can let the program access > more memory to have it run more efficiently or do you suggest I use a > computer with more power?
You should be able to determine if progressiveMauve is running out of memory by looking at a task/process manager. If on linux you could try top, on windows the task manager (via Ctrl+Alt+Esc) or on mac the "Activity Monitor" from the utilities folder. If you see a lot of disk activity, or that the progressiveMauve process is running at much less than 100% CPU, combined with a allocated memory footprint (VM size) approaching your system memory size, then it is likely the program needs more memory. If you don't see those symptoms then it's probably already going as fast as it can as currently implemented. progressiveMauve runs single-threaded (e.g. no multi-core CPU support) and a few days of compute does not sound unusual for a dataset of the size you describe. Best, -Aaron -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email.
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