Pipeline stuck at the tRNAscan step

[gary_xie]

Running bacterial genome on Ergatis pipeline locally, but it stuck at  
the tRNAscan step for 10 days. Following is error message, any insight?
Thanks,
Gary



The Workflow is invoked. View Workflow Monitor to check the progress.
log4j:WARN No appenders could be found for logger  
(org.tigr.antware.shared.util.AppConfig).
log4j:WARN Please initialize the log4j system properly.

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[Mahurkar, Anup]

My guess is that you have a situation where Workflow could not monitor the
job completion status of one of the distributed jobs and hence it is
waiting. One solution is to kill the pipeline and restart. Workflow most
likely will pick up the current state and continue. What version of
workflow are you running? Another option is for us to debug, but in my
experience it is hard to debug without a log file. Could you look for the
pipeline.xml.log and the iterator log file and send it if you want me to
debug.

Anup

On 10/27/11 7:29 PM, "Gary Xie" <[hidden email]> wrote:

>Running bacterial genome on Ergatis pipeline locally, but it stuck at
>the tRNAscan step for 10 days. Following is error message, any insight?
>Thanks,
>Gary


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[Chris Hemmerich]

In addition to the steps Anup mentioned, have you checked to see if the
actual tRNAscan process is still running? I remember that a fasta file
without linebreaks will cause one of the programs (unfortunately, I'm not
sure it was tRNAscan) in the pipeline to run forever.

Cheers,
  Chris


On Thu, 27 Oct 2011, Gary Xie wrote:

> Running bacterial genome on Ergatis pipeline locally, but it stuck at the
> tRNAscan step for 10 days. Following is error message, any insight?
> Thanks,
> Gary
>

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[Roxanne]

It does look like the process is still running, and it looks like it's active, it keeps launching processes trnascan-1.4 and eufindtRNA.   

Roxanne Tapia

Software Developer 3

B-6 Genome Sciences

On Oct 28, 2011, at 10:13 AM, Chris Hemmerich wrote:

In addition to the steps Anup mentioned, have you checked to see if the
actual tRNAscan process is still running? I remember that a fasta file
without linebreaks will cause one of the programs (unfortunately, I'm not
sure it was tRNAscan) in the pipeline to run forever.

Cheers,
 Chris


On Thu, 27 Oct 2011, Gary Xie wrote:

Running bacterial genome on Ergatis pipeline locally, but it stuck at the

tRNAscan step for 10 days. Following is error message, any insight?

Thanks,

Gary

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