Question: STAR genomeLoad issue
0
gravatar for CY
21 months ago by
CY280
United States
CY280 wrote:

I ran STAR in a shared memory environment and tried --genomeLoad LoadAndKeep LoadAndRemove and LoadAndExit hoping one-time reference load can be used by all the samples. However, each sample still load its own reference and memory accumulates in cache and eventual killed job due to insufficient RAM. Can anything share some idea on what is going here? Really appreciated!

By the way. what is the difference between LoadAndRemove and LoadAndExit?

rna-seq • 1.7k views
ADD COMMENTlink modified 21 months ago by h.mon24k • written 21 months ago by CY280
2
gravatar for Devon Ryan
21 months ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

LoadAndExit is convenient if you want to load the genome and then use it in separate STAR runs. It's generally the method I take, since I prefer to loop over samples and not need to keep track of which one is the first one (i.e., I call LoadAndExit first, then make a for loop over samples, and finally call Remove after the for loop).

ADD COMMENTlink written 21 months ago by Devon Ryan88k

Actually I was running two samples almost simultaneously. I thought using LoadAndKeep or LoadAndExit (by the way, what is the difference between these two? I thought both of them are loading the index and keep it in cache) allows the first pipeline load the index and keep it in cache and the second pipeline can use it without loading again. But my test says otherwise...

ADD REPLYlink written 21 months ago by CY280

Well, I retried it in your way and it worked. Thanks Ryan!

ADD REPLYlink written 20 months ago by CY280
0
gravatar for h.mon
21 months ago by
h.mon24k
Brazil
h.mon24k wrote:

It seems either you are loading the genome multiple times or a STAR bug. How are you running the multiple STAR runs? Which version of STAR?

LoadAndRemove will automatically remove the index from memory once all STAR jobs using it finishes. LoadAndExit will leave the index in memory until you run STAR with --genomeLoad Remove.

ADD COMMENTlink written 21 months ago by h.mon24k

So LoadAndExit is the same as LoadAndKeep? Both of these keeps index in memory until run --genomeLoad Remove.

Also, how does STAR know when all STAR jobs finish? I mean if I write a loop, how can STAR know which is the last one?

ADD REPLYlink written 21 months ago by CY280

More or less the same, LoadAndExit does just that, and no mapping whatsoever. LoadAndKeep loads the genome, maps reads and then exits, but leaving the index in memory.

If you use LoadAndExit, STAR doesn't need to know, you will tell STAR when to remove the index after the loop finishes.

ADD REPLYlink written 20 months ago by h.mon24k
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