JalView Memory Issues


When completing exercise 16 in the Manual it suggests to have 256 MB of free memory and download the 1G memory cap version. I did this, yet it still won’t let me load the three sequences from the PFAM (Full) database (PF02008, PF00145, and PF01426). It uses up all of the memory (up to 1GB) when I am viewing the memory usage, and never displays any of the alignments, and comes up with an error message saying there was not enough memory.

Is there a way around this issue? It also won’t let me load more than one individually. I can load a single alignment PF00145, but can’t open a second at the same time.

Thank you,

Kathleen McLeod

Hi Kathleen,

One of the problems with using external alignment databases is that they often increase in size. You need at least 2G (preferably even more) to work with those alignments now. We’re currently updating the manual with up to date memory settings for these sitations - thanks for letting us know about this !

You can launch Jalview with customised memory settings via the JNLP file downloaded with the following link:

(substitute 4G for the maximum amount of memory your machine is able to allocate to Jalview!).



On 17/06/2015 01:18, Kathleen McLeod wrote: