memory Problem With Blat

[mido1951]

hello,
I use BLAT for input data.
but after there has been an error of memory.

[B]needMem: Trying to allocate 543294960 bytes (limit: 500 000 000)[/B]

do you know solve this problem?
thank you

[GenoMax]

How much memory do you have on this machine? Looks like blat is asking for allocation of 543 MB but only 500 MB is available. Is this on 32-bit OS?

[mido1951]

i run this in server with 32GB RAM.
no it is in 64bit Machine

[GenoMax]

In that case check to see if there is a problem with query/database files (a search brought up this thread:http://redmine.soe.ucsc.edu/forum/in...ed756eb8a226ad). What size are those two files (query/database)?

[mido1951]

the size of the query is 3,6GB and the database is 310MB.

[GenoMax]

Can you try switching the query and database around to see if you still get the error?

[mido1951]

it is the same error message.

needMem: Trying to allocate 543294960 bytes (limit: 500 000 000)

do you have another idea?

[GenoMax]

Sounds like you may have some formatting problem with one (or more of your sequences). Use one of the code suggestions here to validate your files: https://www.biostars.org/p/42126/