[maker-devel] debugging

[Barry Moore]

Mike,

Maybe you could send the run.log for this chromosome.  If you've only  
got the one chromosome running then it should just be in a directory  
called "theVoid.*" in the MAKER output directory.  Carson, I wonder if  
it makes sense to inject the path to the run.log in the STDERR output  
when a fatal error (or maybe even any error) occurs?

Barry

On Oct 7, 2009, at 11:21 AM, Reith, Michael wrote:

> Hi,
>
> I've been playing with Maker to get a sense of how it works, etc. and
> ran into a cryptic (to me at least) error.  I was running a chunk of
> Chlamydomonas chromosome 1 (~1.4 Mb) with no repeat masking, a file of
> Chlamy ESTs and a protein database of core eukaryotic genes (cegma)
> which also included Chlamy proteins.  Maker tried twice, but died in  
> the
> same place both times.  Here's the output:
>
> cleaning blastx...
> in cluster:shadow cluster...
>    i_size:0 j_size:0
> sorting hits in shadow cluster...
> ... finished.
> in cluster:shadow cluster...
>    i_size:18 j_size:1
> sorting hits in shadow cluster...
> ... finished.
> i_size:18   current i:0
> i_size:18   current i:1
> i_size:18   current i:2
> i_size:18   current i:3
> i_size:18   current i:4
> i_size:18   current i:5
> i_size:18   current i:6
> i_size:18   current i:7
> i_size:18   current i:8
> i_size:18   current i:9
> i_size:18   current i:10
> i_size:18   current i:11
> i_size:18   current i:12
> i_size:18   current i:13
> i_size:18   current i:14
> i_size:18   current i:15
> i_size:18   current i:16
> i_size:18   current i:17
> cleaning clusters....
> total clusters:1 now processing 0
> ...processing 0 of 11
> ...processing 1 of 11
> ...processing 2 of 11
> ...processing 3 of 11
> ...processing 4 of 11
> ...processing 5 of 11
> ...processing 6 of 11
> ...processing 7 of 11
> ...processing 8 of 11
> ...processing 9 of 11
> #----------------------
> FATAL: failed!!
> #----------------------
> AnyDBM_File doesn't define an EXISTS method
> ERROR: Failed while doing exonerate of proteins!!
>
> ERROR: Chunk failed at level 14
> !!
> FAILED CONTIG:chromosome_1
>
> This appears to have happened with the first 100000 base chunk of the
> sequence - there are blastn and blastx output files that I can send if
> that would be helpful.  Maker was being run on a Sun box under Solaris
> 10.
>
> Thanks for any light you can shed on this.
>
> Mike
>
> -----------------------------------------------------
> Michael Reith
> Principal Research Officer
> Functional Genomics Group Leader
> NRC Institute for Marine Biosciences
> 1411 Oxford St.
> Halifax, N.S.    B3H 3Z1
> Canada
>
> phone:	(902) 426-8276
> fax:	(902) 426-9413
> email:	michael.reith at nrc.ca
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