<HTML>
<HEAD>
<TITLE>Re: [maker-devel] debugging</TITLE>
</HEAD>
<BODY>
<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>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.<BR>
<BR>
Thanks,<BR>
Carson<BR>
<BR>
<BR>
<BR>
On 10/7/09 11:21 AM, "Reith, Michael" <<a href="Michael.Reith@nrc-cnrc.gc.ca">Michael.Reith@nrc-cnrc.gc.ca</a>> wrote:<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Hi,<BR>
<BR>
I've been playing with Maker to get a sense of how it works, etc. and<BR>
ran into a cryptic (to me at least) error. I was running a chunk of<BR>
Chlamydomonas chromosome 1 (~1.4 Mb) with no repeat masking, a file of<BR>
Chlamy ESTs and a protein database of core eukaryotic genes (cegma)<BR>
which also included Chlamy proteins. Maker tried twice, but died in the<BR>
same place both times. Here's the output:<BR>
<BR>
cleaning blastx...<BR>
in cluster:shadow cluster...<BR>
i_size:0 j_size:0<BR>
sorting hits in shadow cluster...<BR>
... finished.<BR>
in cluster:shadow cluster...<BR>
i_size:18 j_size:1<BR>
sorting hits in shadow cluster...<BR>
... finished.<BR>
i_size:18 current i:0<BR>
i_size:18 current i:1<BR>
i_size:18 current i:2<BR>
i_size:18 current i:3<BR>
i_size:18 current i:4<BR>
i_size:18 current i:5<BR>
i_size:18 current i:6<BR>
i_size:18 current i:7<BR>
i_size:18 current i:8<BR>
i_size:18 current i:9<BR>
i_size:18 current i:10<BR>
i_size:18 current i:11<BR>
i_size:18 current i:12<BR>
i_size:18 current i:13<BR>
i_size:18 current i:14<BR>
i_size:18 current i:15<BR>
i_size:18 current i:16<BR>
i_size:18 current i:17<BR>
cleaning clusters....<BR>
total clusters:1 now processing 0<BR>
...processing 0 of 11<BR>
...processing 1 of 11<BR>
...processing 2 of 11<BR>
...processing 3 of 11<BR>
...processing 4 of 11<BR>
...processing 5 of 11<BR>
...processing 6 of 11<BR>
...processing 7 of 11<BR>
...processing 8 of 11<BR>
...processing 9 of 11<BR>
#----------------------<BR>
FATAL: failed!!<BR>
#----------------------<BR>
AnyDBM_File doesn't define an EXISTS method<BR>
ERROR: Failed while doing exonerate of proteins!!<BR>
<BR>
ERROR: Chunk failed at level 14<BR>
!!<BR>
FAILED CONTIG:chromosome_1<BR>
<BR>
This appears to have happened with the first 100000 base chunk of the<BR>
sequence - there are blastn and blastx output files that I can send if<BR>
that would be helpful. Maker was being run on a Sun box under Solaris<BR>
10.<BR>
<BR>
Thanks for any light you can shed on this.<BR>
<BR>
Mike<BR>
<BR>
-----------------------------------------------------<BR>
Michael Reith<BR>
Principal Research Officer<BR>
Functional Genomics Group Leader<BR>
NRC Institute for Marine Biosciences<BR>
1411 Oxford St.<BR>
Halifax, N.S. B3H 3Z1<BR>
Canada<BR>
<BR>
phone: (902) 426-8276<BR>
fax: (902) 426-9413<BR>
email: <a href="michael.reith@nrc.ca">michael.reith@nrc.ca</a><BR>
-----------------------------------------------------------<BR>
The information contained in this e-mail may contain confidential<BR>
information intended for a specific individual and purpose. The<BR>
information is private and is legally protected by law. If you are not<BR>
the intended recipient, you are hereby notified that any disclosure,<BR>
copying, distribution or the taking of any action in reliance on the<BR>
comments of this information is strictly prohibited. If you have<BR>
received this communication<BR>
in error, please notify the sender immediately by telephone or return<BR>
e-mail.<BR>
Thank you.<BR>
<BR>
<BR>
<BR>
_______________________________________________<BR>
maker-devel mailing list<BR>
<a href="maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><BR>
<a href="http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a><BR>
<BR>
</SPAN></FONT></BLOCKQUOTE>
</BODY>
</HTML>