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. ------------------------------------------------------------------------------ The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev _______________________________________________ Ergatis-users mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/ergatis-users |
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 ------------------------------------------------------------------------------ The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev _______________________________________________ Ergatis-users mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/ergatis-users |
In reply to this post by gary_xie
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 > ------------------------------------------------------------------------------ The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev _______________________________________________ Ergatis-users mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/ergatis-users |
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:
------------------------------------------------------------------------------ The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev _______________________________________________ Ergatis-users mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/ergatis-users |
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