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

[Paul C. <pca...@gm...>]

Hi

runCA has moved past the gatekeeper step and is onto the consensus!
Thank you everyone for your help,

Paul

Paul Cantalupo
University of Pittsburgh


On Mon, Aug 27, 2012 at 2:53 PM, Sebastian Jaenicke
<sja...@ce...> wrote:
> 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
>
> --
> A: Maybe because some people are too annoyed by top-posting.
> Q: Why do I not get an answer to my question(s)?
> A: Because it messes up the order in which people normally read text.
> Q: Why is top-posting such a bad thing?