[maker-devel] Early obstacle with SplitDB

[Carson Holt]

Either you speciied TMP= in your maker_opts.ctl file to be an NFS mounted
directory (must be locally mounted), the drive containing directory
specified by TMP= (defaults to /tmp) is full or nearly full, your input file
is not proper fasta format, or you are using an out of date version of
BioPerl.

Try the first three in the list then look at BioPerl.  The BioPerl version
should be printed as part of the the debug output.

--Carson


From:  Kevin Tsai <kevintsai at iis.sinica.edu.tw>
Date:  Tuesday, August 5, 2014 at 4:59 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Early obstacle with SplitDB

Hello,
I'm a new user to Maker so I suspect this will be a simple question, but I
am having trouble finding documentation on SplitDB.  Our IT admin set up the
application and I'm running into the following issue about 30 seconds after
kickoff.  Below is the debugged output:

STATUS: Parsing control files...
Calling GI::load_control_files at /usr/bin/maker line 452.
Calling GI::new_instance_temp at /usr/bin/maker line 463.
Calling GI::mount_check at /usr/bin/maker line 465.
Calling GI::set_global_temp at /usr/bin/maker line 483.
STATUS: Processing and indexing input FASTA files...
Calling GI::s_abs_path at /usr/bin/maker line 519.
Calling GI::s_abs_path at /usr/bin/maker line 519.
Calling GI::s_abs_path at /usr/bin/maker line 519.
Calling GI::s_abs_path at /usr/bin/maker line 519.
Calling GI::s_abs_path at /usr/bin/maker line 519.
Calling List::Util::shuffle at /usr/bin/maker line 529.
Calling GI::split_db at /usr/bin/maker line 536.
Calling File::Path::rmtree at /usr/bin/maker line 537.
Calling Iterator::Any::new at /usr/bin/maker line 537.
Calling Iterator::Any::nextDef at /usr/bin/maker line 537.
Calling Iterator::Any::new at /usr/bin/maker line 537.
Calling mkdir at /usr/bin/maker line 537.
Calling Iterator::Any::nextFastaRef at /usr/bin/maker line 537.
Calling system at /usr/bin/maker line 537.
ERROR: SplitDB not created correctly

 at /usr/local/share/perl5/GI.pm line 1144.
        GI::split_db("/home/keceltes/maker2/final.fasta", "nucleotide", 1,
"/home/keceltes/maker2/final.maker.output/mpi_blastdb", "C") called at
/usr/bin/maker line 537
--> rank=NA, hostname=Za2.cglab

Any suggestions?  Thank you in advance!
-- 
Kevin Tsai
www.linkedin.com/in/kevinjtsai/ <http://www.linkedin.com/in/kevinjtsai/>
Ph.D. Candidate, Bioinformatics
Institute of Information Science, Academia Sinica
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