Forks.pm error when running maker with dsindex

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Forks.pm error when running maker with dsindex

Jan Philip Oeyen
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 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

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: Forks.pm error when running maker with dsindex

Carson Holt-2
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 <[hidden email]>
Date: Monday, July 28, 2014 at 6:22 AM
To: <[hidden email]>
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 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
_______________________________________________ maker-devel mailing list [hidden email] http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: Forks.pm error when running maker with dsindex

Jeanne Wilbrandt
In reply to this post by Jan Philip Oeyen

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, [hidden email] 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 <[hidden email]>
> To: Jan Philip Oeyen <[hidden email]>,
> <[hidden email]>
> Subject: Re: [maker-devel] Forks.pm error when running maker with
> dsindex
> Message-ID: <D005484F.DFD2%[hidden email]>
> 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 <[hidden email]>
> Date:  Monday, July 28, 2014 at 6:22 AM
> To:  <[hidden email]>
> 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
>

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

split_index.o2510 (2K) Download Attachment
maker_04.o2490 (11M) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: Forks.pm error when running maker with dsindex

Carson Hinton Holt
It's better to run fewer jobs with more cpus given to MPI rather than many
jobs with few cpus (i.e. mpiexec -n 4).

To correct errors, you just restart MAKER.  No need to set the -a flag
unless you want to rerun everything, and not just the failed contigs.

--Carson


On 8/6/14, 3:03 AM, "Jeanne Wilbrandt" <[hidden email]> wrote:

>
>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, [hidden email] 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 <[hidden email]>
>> To: Jan Philip Oeyen <[hidden email]>,
>> <[hidden email]>
>> Subject: Re: [maker-devel] Forks.pm error when running maker with
>> dsindex
>> Message-ID: <D005484F.DFD2%[hidden email]>
>> 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 <[hidden email]>
>> Date:  Monday, July 28, 2014 at 6:22 AM
>> To:  <[hidden email]>
>> 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
>>

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org