[maker-devel] Annotation with maker2

[Carson Holt]

Your problem is one of the following.  You need to reinstall the DBD::SQLite
module, you are running in a directory you don’t have permissions for, you
set your TMDIR environmental variable or TMP value in maker_opts.ctl to an
NFS mounted or memory mounted directory, or you are using a self compiled
version of Perl (I.e. not /usr/bin/perl) that has issues (probably with DB
or SQLite modules).  You can also completely delete the output directory,
and start again to see if it was just a random error.  You should look at
each of those first.  You can also run MAKER with the --debug command line
flag and send it to me if all of those seem not to be the issue.

Thanks,
Carson


From:  Chris Bioinfo <chrisbioinfo at gmail.com>
Date:  Wednesday, March 19, 2014 at 5:09 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Annotation with maker2

Hello,

I'm installing/using maker2 for the first time and I have an error by using
it.

I certainly missing something, but I don't know what.

I compile maker with no error message and I have all these directories after
compilation: 
bin  data  GMOD  INSTALL  lib  LICENSE  MWAS  perl  README  src

Nevertheless when I try maker2 on the test data (dpp_contig.fasta) I have
this error:

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: contig-dpp-500-500
Length: 32156
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
DBI connect('dbname=/path/to/dpp_contig.maker.output/dpp_contig.db','',...)
failed: unable to open database file at
/usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm

Can't call method "do" on an undefined value at
/usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm
--> rank=NA, hostname=belem
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500
...

ideas?

Best,

Christelle

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