[maker-devel] debugging

[Mark Yandell]

Ahh there's the quick answer....


Mark Yandell
Associate Professor of Human Genetics
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707
________________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Carson Holt
Sent: Wednesday, October 07, 2009 1:24 PM
To: Reith, Michael; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] debugging

The AnyDBM_File is related to the fasta index which is being built by BioPerl.  First, make sure you have BioPerl 1.6 installed and not 1.5 (MAKER requires version 1.6).  1.5 will fail with weird indexing errors.  Then if you install the new BioPerl 1.6, re-run MAKER with the –f option on the command line so all old indexes and run data get destroyed and rebuilt.  BioPerl uses AnyDBM for communication with Berkley DB by default.  Most systems should already have Berkley DB (redhat, ubuntu, etc.), but you may want to check with whoever manages your system to make sure.  Also make sure you have the most recent version of MAKER from the lab website.  After trying again, let me know if it works.

Thanks,
Carson



On 10/7/09 11:21 AM, "Reith, Michael" <Michael.Reith at nrc-cnrc.gc.ca> 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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