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<div>That can happen on some systems with that very old version of MAKER. Use MAKER 2.28 or 2.30 instead —> <a href="http://www.yandell-lab.org/software/maker.html">http://www.yandell-lab.org/software/maker.html</a></div>
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<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>"Cexzur Jimenez Jr." <<a href="mailto:cexzurjimenezjr@gmail.com">cexzurjimenezjr@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, February 6, 2014 at 10:27 PM<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] Testing MAKER After Installation<br>
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<div>Hello,<br>
<br>
</div>
I have finished installing MAKER marked by "PERL Dependencies: INSTALLED, External Programs: INSTALLED, MPI SUPPORT: NOT CONFIGURED,<br>
MAKER: INSTALLED" and it seems everything's fine. I'm using MAKER 2.10 and I have followed the installation instructions both in its corresponding "README" and "INSTALL" files and the 2012 GMOD MAKER Tutorial. After editing the three configuration files and
run with "maker", I saw the following error in my terminal. I have searched Google and tried the solutions offered there but the error is still showing. Below is the error I got:<br>
<br>
<div>
<div><br>
Can't locate package GDBM_File for @AnyDBM_File::ISA at /usr/lib/perl/5.14/DB_File.pm line 287.<br>
Can't locate package NDBM_File for @AnyDBM_File::ISA at /usr/lib/perl/5.14/DB_File.pm line 287.<br>
Can't locate package SDBM_File for @AnyDBM_File::ISA at /usr/lib/perl/5.14/DB_File.pm line 287.<br>
A data structure will be created for you at:<br>
/home/cexzurjimenezjr/Documents/data/dpp_contig.maker.output/dpp_contig_datastore<br>
<br>
To access files for individual sequences use the datastore index:<br>
/home/cexzurjimenezjr/Documents/data/dpp_contig.maker.output/dpp_contig_master_datastore_index.log<br>
<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>
running repeat masker.<br>
#--------- command -------------#<br>
Widget::RepeatMasker:<br>
/usr/local/maker/exe/RepeatMasker/RepeatMasker /home/cexzurjimenezjr/Documents/data/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/cexzurjimenezjr/Documents/data/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500
-pa 1<br>
#-------------------------------#<br>
Building general libraries in: /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general<br>
RepeatMasker::createLib(): Error invoking /usr/local/blast/bin/makeblastdb on file /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general/at.lib.<br>
ERROR: RepeatMasker failed<br>
<br>
FATAL ERROR<br>
ERROR: Failed while doing repeat masking!!<br>
<br>
ERROR: Chunk failed at level 2<br>
!!<br>
FAILED CONTIG:contig-dpp-500-500<br>
<br>
<br>
<br>
<br>
--Next Contig--<br>
<br>
Processing run.log file...<br>
MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb.out<br>
did not finish on the last run and must be erased<br>
#---------------------------------------------------------------------<br>
Now retrying the contig!!<br>
SeqID: contig-dpp-500-500<br>
Length: 32156<br>
Retry: 1!!<br>
#---------------------------------------------------------------------<br>
<br>
<br>
running repeat masker.<br>
#--------- command -------------#<br>
Widget::RepeatMasker:<br>
/usr/local/maker/exe/RepeatMasker/RepeatMasker /home/cexzurjimenezjr/Documents/data/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/cexzurjimenezjr/Documents/data/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500
-pa 1<br>
#-------------------------------#<br>
Building general libraries in: /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general<br>
RepeatMasker::createLib(): Error invoking /usr/local/blast/bin/makeblastdb on file /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general/at.lib.<br>
ERROR: RepeatMasker failed<br>
<br>
FATAL ERROR<br>
ERROR: Failed while doing repeat masking!!<br>
<br>
ERROR: Chunk failed at level 2<br>
!!<br>
FAILED CONTIG:contig-dpp-500-500<br>
<br>
<br>
<br>
<br>
--Next Contig--<br>
<br>
Processing run.log file...<br>
MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb.out<br>
did not finish on the last run and must be erased<br>
<br>
<br>
Maker is now finished!!!<br>
<br>
<br>
</div>
<div>Can you state to me the error and what part of the installation did I go wrong? Your help will be very much appreciated. Thank you.<br>
<br>
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<div>Attached herein are configuration files I used for MAKER.<br>
<br>
<br>
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<div>Sincerely,<br>
<br>
</div>
<div>CJ<br>
</div>
<div><br>
</div>
</div>
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