<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>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.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Chris Bioinfo <<a href="mailto:chrisbioinfo@gmail.com">chrisbioinfo@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, March 19, 2014 at 5:09 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Annotation with maker2<br></div><div><br></div><div dir="ltr"><div><div><div>Hello,<br><br></div>I'm installing/using maker2 for the first time and I have an error by using it.<br><br></div>I certainly missing something, but I don't know what.<br><br></div>I compile maker with no error message and I have all these directories after compilation: <br><div><div><div><div>bin data GMOD INSTALL lib LICENSE MWAS perl README src<br><br></div><div>Nevertheless when I try maker2 on the test data (dpp_contig.fasta) I have this error:<br><br></div><div>STATUS: Now running MAKER...<br>
examining contents of the fasta file and run log<br><br><br><br>--Next Contig--<br><br>#---------------------------------------------------------------------<br>Now starting the contig!!<br>SeqID: contig-dpp-500-500<br>Length: 32156<br>
#---------------------------------------------------------------------<br><br><br>setting up GFF3 output and fasta chunks<br>doing repeat masking<br>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<br><br>Can't call method "do" on an undefined value at /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm <br>--> rank=NA, hostname=belem<br>ERROR: Failed while doing repeat masking<br>ERROR: Chunk failed at level:0, tier_type:1<br>
FAILED CONTIG:contig-dpp-500-500<br>...<br><br></div><div>ideas?<br></div><div><br></div><div>Best,<br><br></div><div>Christelle<br></div><div><br></div></div></div></div></div>
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