Testing MAKER After Installation

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Testing MAKER After Installation

Cexzur Jimenez Jr.
Hello,

I have finished installing MAKER marked by "PERL Dependencies: INSTALLED, External Programs: INSTALLED, MPI SUPPORT: NOT CONFIGURED,
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:


Can't locate package GDBM_File for @AnyDBM_File::ISA at /usr/lib/perl/5.14/DB_File.pm line 287.
Can't locate package NDBM_File for @AnyDBM_File::ISA at /usr/lib/perl/5.14/DB_File.pm line 287.
Can't locate package SDBM_File for @AnyDBM_File::ISA at /usr/lib/perl/5.14/DB_File.pm line 287.
A data structure will be created for you at:
/home/cexzurjimenezjr/Documents/data/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/home/cexzurjimenezjr/Documents/data/dpp_contig.maker.output/dpp_contig_master_datastore_index.log




--Next Contig--

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


running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
/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
#-------------------------------#
Building general libraries in: /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general
RepeatMasker::createLib(): Error invoking /usr/local/blast/bin/makeblastdb on file /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general/at.lib.
ERROR: RepeatMasker failed

FATAL ERROR
ERROR: Failed while doing repeat masking!!

ERROR: Chunk failed at level 2
!!
FAILED CONTIG:contig-dpp-500-500




--Next Contig--

Processing run.log file...
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
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: contig-dpp-500-500
Length: 32156
Retry: 1!!
#---------------------------------------------------------------------


running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
/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
#-------------------------------#
Building general libraries in: /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general
RepeatMasker::createLib(): Error invoking /usr/local/blast/bin/makeblastdb on file /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general/at.lib.
ERROR: RepeatMasker failed

FATAL ERROR
ERROR: Failed while doing repeat masking!!

ERROR: Chunk failed at level 2
!!
FAILED CONTIG:contig-dpp-500-500




--Next Contig--

Processing run.log file...
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
did not finish on the last run and must be erased


Maker is now finished!!!


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.

Attached herein are configuration files I used for MAKER.


Sincerely,

CJ


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Re: Testing MAKER After Installation

Carson Hinton Holt
That can happen on some systems with that very old version of MAKER.  Use MAKER 2.28 or 2.30 instead —> http://www.yandell-lab.org/software/maker.html

Thanks,
Carson


From: "Cexzur Jimenez Jr." <[hidden email]>
Date: Thursday, February 6, 2014 at 10:27 PM
To: <[hidden email]>
Subject: [maker-devel] Testing MAKER After Installation

Hello,

I have finished installing MAKER marked by "PERL Dependencies: INSTALLED, External Programs: INSTALLED, MPI SUPPORT: NOT CONFIGURED,
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:


Can't locate package GDBM_File for @AnyDBM_File::ISA at /usr/lib/perl/5.14/DB_File.pm line 287.
Can't locate package NDBM_File for @AnyDBM_File::ISA at /usr/lib/perl/5.14/DB_File.pm line 287.
Can't locate package SDBM_File for @AnyDBM_File::ISA at /usr/lib/perl/5.14/DB_File.pm line 287.
A data structure will be created for you at:
/home/cexzurjimenezjr/Documents/data/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/home/cexzurjimenezjr/Documents/data/dpp_contig.maker.output/dpp_contig_master_datastore_index.log




--Next Contig--

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


running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
/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
#-------------------------------#
Building general libraries in: /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general
RepeatMasker::createLib(): Error invoking /usr/local/blast/bin/makeblastdb on file /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general/at.lib.
ERROR: RepeatMasker failed

FATAL ERROR
ERROR: Failed while doing repeat masking!!

ERROR: Chunk failed at level 2
!!
FAILED CONTIG:contig-dpp-500-500




--Next Contig--

Processing run.log file...
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
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: contig-dpp-500-500
Length: 32156
Retry: 1!!
#---------------------------------------------------------------------


running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
/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
#-------------------------------#
Building general libraries in: /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general
RepeatMasker::createLib(): Error invoking /usr/local/blast/bin/makeblastdb on file /usr/local/maker/exe/RepeatMasker/Libraries/20120418/general/at.lib.
ERROR: RepeatMasker failed

FATAL ERROR
ERROR: Failed while doing repeat masking!!

ERROR: Chunk failed at level 2
!!
FAILED CONTIG:contig-dpp-500-500




--Next Contig--

Processing run.log file...
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
did not finish on the last run and must be erased


Maker is now finished!!!


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.

Attached herein are configuration files I used for MAKER.


Sincerely,

CJ

_______________________________________________ maker-devel mailing list [hidden email] http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org