[maker-devel] debugging

[Reith, Michael]

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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