[maker-devel] Early obstacle with SplitDB

Wed Aug 13 11:14:56 MDT 2014

On Aug 11, 2014, at 11:11 AM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:

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?

Exactly.  Just a note, but the CPAN releases (now at 1.6.924) merge over all changes from the master branch on a regular basis.  The key parts that will not work when running off master (such as Bio::Root, Bio::FeatureIO, etc) have been split out into separate repos; it’s entirely possible to add these separately to a PERL5LIB but the intent is that we will release Bio-Root and others to CPAN separately.

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.

Re: Berkeley_DB, if you have a need to push this in a more NFS-portable direction we are more than happy to let you experiment on what works best.  Mark Jensen actually started on this a while back but ran into problems.

I personally haven’t had problems with Bio::DB::Fasta on our local GPFS to be frank, but I’m sure that isn’t working for everyone.

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

chris

From: Kevin Tsai <kevintsai at iis.sinica.edu.tw<mailto:kevintsai at iis.sinica.edu.tw>>
Date: Monday, August 11, 2014 at 5:11 AM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Cc: <maker-devel at yandell-lab.org<mailto: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<mailto: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<mailto:kevintsai at iis.sinica.edu.tw>>
Date: Tuesday, August 5, 2014 at 4:59 AM
To: <maker-devel at yandell-lab.org<mailto: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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--
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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