Re: [wgs-assembler-users] gatekeeper failed - too many open files

[Sebastian J. <sja...@Ce...>]

Hi,

On Mon, Aug 27, 2012 at 11:51:45AM -0400, Paul Cantalupo wrote:
[..]
> I'm trying to assemble a 4.4 Gb fastq file containing ~8.3 million 454
> sequences. I'm using runCA version 7.0 on a Mac Server Snow Leopard
> 10.6. I got an error that says "to many open files" (see attached
> error.txt file). I've attached the spec file as well.

try rising the number of open files permitted by your system; I don't
know the defaults for Snow Leopard, but 2048 should be sufficient.
I.e., invoke

    ulimit -n 2048

before runCA. You can check defaults with just 'ulimit -n'.

Regards,

- Sebastian

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