BLAT - out of memory

[sathish]

Hi Everyone,

When I try to do UCSC BLAT, I am getting the following error.

needLargeMem: Out of memory - request size 536 bytes

Error: Blat Failed


I also increased my computer memory from 8 GB to 24 GB. Still I am getting this error. Is there any other way other than trying to split the database file into small files for Blat?

Any help will be appreciated.

Thanks,

Sathish

[adamdeluca]

I have seen memory errors like that from UCSC utilities when they are piped an empty file.

Otherwise splitting your reference is the way to go.

[Torst]

When I try to do UCSC BLAT, I am getting the following error. needLargeMem: Out of memory - request size 536 bytes Error: Blat Failed I also increased my computer memory from 8 GB to 24 GB. Still I am getting this error. Is there any other way other than trying to split the database file into small files for Blat?

Just to check - did you install a 64 bit operating system (x86_64, not i386) and is blat compiled as a 64-bit executable?

You can check the binary using the "file" command:

% cd /path/to/blat/folder/
% file blat
blat: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.4.0

[RDW]

Can you use the gfServer and gfClient binaries rather than the standalone blat binary? gfServer builds an index of a more manageable size from your database and makes it available for queries by gfClient. Using (e.g.) hg18.2bit as input, you should be able to run whole genome queries even on a 32-bit system with 2Gb RAM.

[aquinom85]

I'm running blat on a server with 32GB of RAM and I get this error
{0}: blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 hgnochr19.2bit query.fa output.ps1Loaded 3137161262 letters in 93 sequences
needHugeMen: Out of huge memory - request size 2117024308 bytes

Aside from the humorous error message, it's saying the request is 2 GB and running out of RAM I don't see how this is possible. Is there a way to allocate extra RAM to a C++ executable like you can with java?

[westerman]

Aside from the humorous error message, it's saying the request is 2 GB and running out of RAM I don't see how this is possible. Is there a way to allocate extra RAM to a C++ executable like you can with java?

Admittedly I am not a Java expert but in my experience Java is the one of the few cases where you *have* to pre-allocate memory. Other languages are, in my opinion, much more sensible being effectively unlimited in memory (up to the system's overall memory).

In other words when you start up Java you *must* allocate the memory it is going to use via the '-Xm' parameters. If you go over that allocation, no matter how much system memory you might have, then Java will crash with "out of memory".

Other languages will keep requesting more memory from the system (usually through some variant of malloc) until the system gives them an error. I suspect that this is what you are encountering. In other words the system *is* actually out of memory and when Blat wants another 2GB then then system says "no way" and then Blat reports this back to you.

BTW: You could also be running into a 32-bit binary limitation on memory. As 'torst' said, check your binary.