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

[Carson Holt]

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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