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

[Krishnakumar, Vivek]

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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130123/224026a7/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: attachment-24.png
Type: image/png
Size: 641 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130123/224026a7/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: dropbox.png
Type: image/png
Size: 1205 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130123/224026a7/attachment-0005.png>