[ensembl-dev] pipeline run with status 'VOID'

Susan Fairley sf7 at sanger.ac.uk
Fri Jun 10 13:44:38 BST 2011


With certain sequences, it isn't possible for Genscan to run (i.e. Need
at least 3 nucleotides...). When a Genscan job encounters such a case,
it returns VOID, as you have seen. This indicates that Genscan didn't
'FAIL' due to, for example, a lack of resources but that it wasn't
possible for it to attempt to make predictions due to the sequence it
was running on.

When this happens, it is worth checking that you are happy that there is
a reason the job is VOID (which you seem to have done). If so, and
assuming rule_manager.pl isn't running, you can remove the jobs from the
pipeline (they exist in the job and job_status tables and will be
is_current='y' and status='VOID'). Otherwise, the jobs will remain
listed as VOID when you monitor the progress of your jobs.

I hope this helps.


江JWK wrote:
> Hi
> I have try to test the genebuild pipeline,
> the analysis i used are repeatmask, genscan, trf,
> but after all other jobs are finished, i have three jobs with status "VOID":
>  12235 VOID     2011-06-10 17:21:23 y         
> I check the stderr file for these jobs, and found that :
> Running job 12235
> Module is Genscan
> input id is XXX
> Analysis is Genscan
> Need at least 3 nucleotides - maybe your sequence was fully repeatmasked ...
> ...
> ...
> Updated successful job 12235
> Finished job 12235
> My question is that 'VOID' stands for what?
> Now the pipeline stop at this point for hours, any suggestions?
> ------------------------------------------------------------------------
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

More information about the Dev mailing list