[maker-devel] Forks.pm error when running maker with dsindex

[Jeanne Wilbrandt]

Hi!

Yes, we are running 20 jobs simultaneously, almost, i.e., as much as our cluster can
take. Do you think this is too much?

Please find attached the output file (containing the STDERR) of the dsindex-run, and one
example output of one of the pieces.

Another quick question to make sure I understood the guides correctly: If a job did not
finish properly, it should suffice to restart the same thing just with the -a flag and it
should clean up and finish what it was supposed to, right? (i.e., it's not necessary to
trace and delete the unfinished output manually?)

Thank you again!
Jeanne Wilbrandt

zmb // ZFMK // University of Bonn



On 08/05/2014 08:00 PM, maker-devel-request at yandell-lab.org wrote:
>
>
>    1. Re: Forks.pm error when running maker with dsindex (Carson Holt)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 04 Aug 2014 14:27:08 -0600
> From: Carson Holt <carsonhh at gmail.com>
> To: Jan Philip Oeyen <jp.oeyen at uni-bonn.de>,
> 	<maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Forks.pm error when running maker with
> 	dsindex
> Message-ID: <D005484F.DFD2%carsonhh at gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Sorry for the slow reply.  I was on vacation all last week.  Do you have the
> full STDERR? sometimes the last error is irrelevant and it's just the result
> of a failure further upstream. Also are you running 20 independent maker
> jobs simultaneously?
>
> --Carson
>
>
> From:  Jan Philip Oeyen <jp.oeyen at uni-bonn.de>
> Date:  Monday, July 28, 2014 at 6:22 AM
> To:  <maker-devel at yandell-lab.org>
> Subject:  [maker-devel] Forks.pm error when running maker with dsindex
>
> Hi all,
> we are currently having some unexpected errors when running maker on a
> genome which is split in several parts. Our cluster admin reported the
> following error message:
>
> Argument "ALRM" isn't numeric in exit at /share/scientific_bin/perlmodu
> les/lib/site_perl/5.14.2/x86_64-linux-thread-multi/forks.pm
> <http://forks.pm>  line 2188.
> SIGTERM received
> SIGTERM received
> SIGTERM received
>
> We were using maker with the '-g' option on a single genome which is split
> into 20 parts, where 19 parts are equally large and the last contains about
> 20 sequences more. After that we ran Maker using dsindex to clean up the
> output. We are currently using maker v2.31 on 4 threads and forks v0.34.
>
> If any further info is needed to clarify the problem, please let me know and
> I will provide as much as possible.
>
> Thank you for your help!
>
> Best regards,
> Jan Philip Oeyen
> ZFMK // ZMB // University of Bonn
>
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