Entering edit mode
5.5 years ago
griffinwhy
•
0
I'm using MEGAX's ClustalW to align 319 variants of the rabies virus, each about 12,000 bp. It's been running for a few days and recently reached the end of the "Pairwise Align" bar, but has not progressed from there into the "Multiple Alignment" bar for the last 12 or so hours. Any idea why this might be?
A "hand wavy" comment (like what follows) is likely the best we can do in this case. Is this question about program the
MEGAor is there a program calledMEGAXsomewhere?We have no idea what kind of hardware you are running this on, if you have successfully tested this program before with a smaller dataset to make sure the program itself works. In general, if something is taking "days" to run (you don't say how many) then consider it an indication to look for either alternate hardware or a program. A large alignment like this is best done on a server with plenty of RAM and cores.
That said, if
Task Manager/Activity Monitor/top(depending on the OS you are running this on) shows MEGA consuming CPU cycles then you may want to wait for some more time to see what happens.