[maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI

[Carson Holt]

If you still see issue, let me know.  I  have a hard time seeing how just
moving to MPICH2 would have solved the issue. It may also have been an
initial problem with the first GFF# db being created and running on a new
job recreated it correctly.  Either way, let me know if it comes up on your
bigger run.

Thanks,
Carson


From:  "Krishnakumar, Vivek" <vkrishnakumar at jcvi.org>
Date:  Thursday, 24 January, 2013 2:49 PM
To:  <maker-devel at yandell-lab.org>, <mcampbell at genetics.utah.edu>
Subject:  Re: [maker-devel] DBD::SQLite::db do failed: database is locked
(GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI

    
 Hi Everybody,
 
 Sorry for jumping the gun and writing to the mailing list before completely
troubleshooting this issue. I was able to figure out the problem and get
MAKER 2.27b working fine in MPI mode.
 
 The issue was with the incorrect version of mpicc (it was openMPI based and
not mpich2). I was able to successfully run through the steps described
below on one chromosome in under a few hours (~2). Now I'm scaling it to the
whole genome (8 chromosomes and ~2200 unanchored scaffolds).
 
 Thank you.
 Vivek
 
 
On 01/23/2013 02:42 PM, Krishnakumar, Vivek wrote:
 
 
>   Hello,
>  
>  I'm trying to use the MAKER pipeline to calculate AED scores for the gene
> models coming out of our annotation pipeline (EVidence Modeler). We then want
> to compare these computed AED scores with those computed for the gene models
> coming out of the MAKER2 pipeline.
>  
>  For this purpose, I configured the maker_opts.ctl file like so:
>  1) Specify gff file coming from our annotation pipeline using `model_gff`
> param 
>  2) Specify gff file containing est2genome results (computed using MAKER2)
> using the `est_gff` param
>  3) Specify gff file containing protein2genome results (computed using MAKER2)
> using the `protein_gff` param
>  4) Specify the genome fasta sequence file using the `genome` param
>  
>  I recently configured MAKER 2.27b to work using MPI and I tried launching one
> contig (chromosome) on a compute node spawning 12 processes like so:
>  mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl maker_bopts.ctl
> maker_exe.ctl 2>&1 | tee maker.err
>  
>  Side note: Without MPI, it works fine but takes very very long to complete
> running on one chromosome (since it is going through the chunks serially).
>  
>  On inspecting the `maker.err` file, I see server error messages that say
> `DBD::SQLite::db do failed: database is locked`. On referring to a previous
> email thread on the `maker-devel` mailing list, I see that Carson had replied
> to the person with a similar issue asking them to check if the working
> directory and TMP directory are being mounted on an NFS filesystem because
> this is a potential problem with SQLite databases.
>  
>  Based on that suggestion, I switched the TMP directory to use a local
> filesytem but the working directory is still NFS mounted. Despite that, I
> still get this error. The previous email thread had no resolution for this
> issue. My question is, should the working directory be local as well? I see
> that despite setting the `TMP` variable, the SQLite DB is getting created in
> the working directory.
>  
>  What might be the issue?
>  
>  Also, apart from this one error, I notice another error:
>  ERROR: Non-unique top level ID for chr5:hit:1454:4_0
>  While this is technically legal in GFF3, it usually
>  indicates a poorly fomatted GFF3 file (perhaps you
>  tried to merge two GFF3 files without accounting for
>  unique IDs).  MAKER will not handle these correctly.
>  
>  On inspecting the input GFF file (protein2genome), I see that this ID is
> never repeated. So I have no idea whats going on here either. Any suggestions?
>  
>  Below is my `maker.err` file from the run. (Dropbox link)
>  
>  Thank you very much.
>  Best,
>  
>  Vivek
>  
>  --
>  Vivek Krishnakumar
>  vkrishnakumar at jcvi.org
>  
>  
>  
> I've linked 1 file to this email:
>  
>  
> maker.err <http://db.tt/2tYyKCD7> (97.7  MB)Dropbox <https://www.dropbox.com/>
> http://db.tt/2tYyKCD7
>  
>  
> Mozilla Thunderbird <http://www.getthunderbird.com>  makes it easy to share
> large files over email.
>  
>  
>  
 
 
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130124/22d9a19a/attachment-0003.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Preview.app Document
Type: image/png
Size: 641 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130124/22d9a19a/attachment-0006.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Preview.app Document
Type: image/png
Size: 1205 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130124/22d9a19a/attachment-0007.png>