Pipeline failure/restart

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Pipeline failure/restart

Roxanne
Hi,

I was running a version of the Prokaryotic Annotation Pipeline without Loading, and it got as far as tmmhmm.default.  There were only a few errors- 13 of 607 actions.  
I get a message that the return value was 141.  The std err and std out files were empty.

When I cut and paste the command on the server, I get no error message, but the output file is empty.  It looks like the input file exists, and is fine.  

So my questions:

1) Anyone know how to fix this problem, or if it is really a problem? If it's not really a problem, how to have ergatis deal with the return value?
2) How to restart a pipeline in mid-execution (from where it failed, or right after)?

Thanks!
Roxanne




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Re: Pipeline failure/restart

Joshua Orvis
Roxanne -

I've experienced this problem with tmmhmm - executions on random nodes returning an error code but re-running is successful, often even on the same node.  I tried the same things you did regarding running it manually and received no errors.  Restarting the pipeline the pipeline would fix the problem, and I'd spend some time trying to figure out if the nodes it failed on were somehow different from the ones it didn't but didn't get anywhere.

Regarding restarting a pipeline, anytime you click the 'rerun' button at the top of a pipeline view page it will always skip forward through any completed commands and restart from the point of failure - any non-complete state, and carry on from there. 

Joshua


On Tue, Aug 9, 2011 at 11:29 AM, Roxanne Tapia <[hidden email]> wrote:
Hi,

I was running a version of the Prokaryotic Annotation Pipeline without Loading, and it got as far as tmmhmm.default.  There were only a few errors- 13 of 607 actions.
I get a message that the return value was 141.  The std err and std out files were empty.

When I cut and paste the command on the server, I get no error message, but the output file is empty.  It looks like the input file exists, and is fine.

So my questions:

1) Anyone know how to fix this problem, or if it is really a problem? If it's not really a problem, how to have ergatis deal with the return value?
2) How to restart a pipeline in mid-execution (from where it failed, or right after)?

Thanks!
Roxanne




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Re: Pipeline failure/restart

Roxanne
Actually,  ti was tmhmm configuration - a lot of hard-coded paths in the tmhmmformat.pl script . So, I think we've got it running now.  I'm about to retry the rerun. 
Thanks!

Roxanne Tapia
Software Developer 3
B-6, Genome Science
Bioscience Division
(505)665-0206




On Aug 9, 2011, at 10:57 AM, Joshua Orvis wrote:

Roxanne -

I've experienced this problem with tmmhmm - executions on random nodes returning an error code but re-running is successful, often even on the same node.  I tried the same things you did regarding running it manually and received no errors.  Restarting the pipeline the pipeline would fix the problem, and I'd spend some time trying to figure out if the nodes it failed on were somehow different from the ones it didn't but didn't get anywhere.

Regarding restarting a pipeline, anytime you click the 'rerun' button at the top of a pipeline view page it will always skip forward through any completed commands and restart from the point of failure - any non-complete state, and carry on from there. 

Joshua


On Tue, Aug 9, 2011 at 11:29 AM, Roxanne Tapia <[hidden email]> wrote:
Hi,

I was running a version of the Prokaryotic Annotation Pipeline without Loading, and it got as far as tmmhmm.default.  There were only a few errors- 13 of 607 actions.
I get a message that the return value was 141.  The std err and std out files were empty.

When I cut and paste the command on the server, I get no error message, but the output file is empty.  It looks like the input file exists, and is fine.

So my questions:

1) Anyone know how to fix this problem, or if it is really a problem? If it's not really a problem, how to have ergatis deal with the return value?
2) How to restart a pipeline in mid-execution (from where it failed, or right after)?

Thanks!
Roxanne




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Re: Pipeline failure/restart

Joshua Orvis
That's interesting.  If there were hard-coded values that were causing failures I would have expected that cause failures in ALL of the executions, not just 13 out of 607.  Glad you've got it running.

JO



2011/8/9 Roxanne Tapia <[hidden email]>
Actually,  ti was tmhmm configuration - a lot of hard-coded paths in the tmhmmformat.pl script . So, I think we've got it running now.  I'm about to retry the rerun. 
Thanks!

Roxanne Tapia
Software Developer 3
B-6, Genome Science
Bioscience Division
<a href="tel:%28505%29665-0206" value="+15056650206" target="_blank">(505)665-0206




On Aug 9, 2011, at 10:57 AM, Joshua Orvis wrote:

Roxanne -

I've experienced this problem with tmmhmm - executions on random nodes returning an error code but re-running is successful, often even on the same node.  I tried the same things you did regarding running it manually and received no errors.  Restarting the pipeline the pipeline would fix the problem, and I'd spend some time trying to figure out if the nodes it failed on were somehow different from the ones it didn't but didn't get anywhere.

Regarding restarting a pipeline, anytime you click the 'rerun' button at the top of a pipeline view page it will always skip forward through any completed commands and restart from the point of failure - any non-complete state, and carry on from there. 

Joshua


On Tue, Aug 9, 2011 at 11:29 AM, Roxanne Tapia <[hidden email]> wrote:
Hi,

I was running a version of the Prokaryotic Annotation Pipeline without Loading, and it got as far as tmmhmm.default.  There were only a few errors- 13 of 607 actions.
I get a message that the return value was 141.  The std err and std out files were empty.

When I cut and paste the command on the server, I get no error message, but the output file is empty.  It looks like the input file exists, and is fine.

So my questions:

1) Anyone know how to fix this problem, or if it is really a problem? If it's not really a problem, how to have ergatis deal with the return value?
2) How to restart a pipeline in mid-execution (from where it failed, or right after)?

Thanks!
Roxanne




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