RAM Usage Issue when Construction Genetic Map

[Melissa Lehrer]

Hi Dr. Broman,

I apologize that this question is not directly related to R/qtl itself, but I have been unable to find helpful a response online, especially one related to Mac operating systems, and was hoping you may have some insight based on your experience and expertise. 

I am in this process of constructing a genetic map for Sorghum, with 10 chromosomes and just over 2000 markers. I am using RStudio (version 1.4.1717) on a MacBook Pro with 16GB of RAM. I am in the process of ordering the markers on each chromosome (i.e. filename = orderMarkers(filename, chr= chromosome number)). I've been able to order the markers on chromosomes 2-10 (I started from 10 and worked my way up), and am now trying to order the markers on chromosome 1. However, about 30 minutes (I am also not sure if this process usually takes this long; so far, it usually takes about an hour and a half) in to executing this process, I get the following error: Error: vector memory exhausted (limit reached?).

When monitoring the memory using executing this code, I quickly realized that all 16GB of RAM are being used during this time. Strangely, the genetic map file in RStudio is only 40MB, and there is still plenty of available memory in RStudio itself, so I am unsure of how to solve this issue. 

Any advice would be greatly appreciate, as this issue has really thrown a wrench in my analysis. 

Thank you,

   Melissa 

[Karl Broman]

The only thing I can think of in orderMarkers that could use a lot of memory would be ripple to permute markers in a sliding window,

So maybe try use.ripple=FALSE, or window=3 (rather than =7 which is the default).

karl