[maker-devel] Early obstacle with SplitDB

[Carson Holt]

If you are updating every month to BioPerl live, don't.  You should use the
CPAN version of BioPerl or even the stable download.  BioPerl live has
actually broken several components MAKER uses at different times and
depending on which version you currently have, may be broken now.  Could you
send me the Bio::Root::Version line from the initial debug output?

Also could you send me this file --> /home/keceltes/maker2/final.fasta

The point of failure is actually very simple.  At that point in the code,
MAKER opens a file, reads it in one line at a time, writes it out to a new
file, and then indexes it with BioPerl (the BioPerl won't work with NFS
drives because it uses Berkley DB).  For that reason whenever it fails at
that point, it is either a drive space issue, NFS issue, BioPerl issue, or
file format issue.

Also are you running via MPI? I ask because if you are using multiple nodes
you will have to check the sixe of /tmp independently on each node (since
the values will be different).

Thanks,
Carson

From:  Kevin Tsai <kevintsai at iis.sinica.edu.tw>
Date:  Monday, August 11, 2014 at 5:11 AM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Early obstacle with SplitDB

Hi Carson,
Thanks for the suggestions.

I left the TMP= empty, which as you mentioned defaults to /tmp.  There seems
to be a different error when using an NFS mounted directory (as I manually
verified).  My /tmp is also not full or nearly full, I have verified proper
fasta formatting as I have run the fasta file through other statistics
generating tools (i.e. Quast).  We are also update BioPerl monthly.

Do you think it could be anything else?  Do you think any more information
that I might be able to provide will be more insightful?


On Tue, Aug 5, 2014 at 1:26 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 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 proper fasta format, or you are using an out of date version of BioPerl.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
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org



-- 
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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