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

[Krishnakumar, Vivek]

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.
>

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