<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>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.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> "Krishnakumar, Vivek" <<a href="mailto:vkrishnakumar@jcvi.org">vkrishnakumar@jcvi.org</a>><br><span style="font-weight:bold">Date: </span> Thursday, 24 January, 2013 2:49 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>, <<a href="mailto:mcampbell@genetics.utah.edu">mcampbell@genetics.utah.edu</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] DBD::SQLite::db do failed: database is locked (GFFDB.pm lines 407, 408, 497) error - Using MAKER 2.27b MPI<br></div><div><br></div><div>
<meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type">
<div bgcolor="#FFFFFF" text="#000000">
Hi Everybody,<br>
<br>
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. <br>
<br>
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).<br>
<br>
Thank you.<br>
Vivek<br>
<br>
<div class="moz-cite-prefix">On 01/23/2013 02:42 PM, Krishnakumar,
Vivek wrote:<br>
</div>
<blockquote cite="mid:51003D32.4080908@jcvi.org" type="cite">
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
Hello,<br>
<br>
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.<br>
<br>
For this purpose, I configured the maker_opts.ctl file like so:<br>
1) Specify gff file coming from our annotation pipeline using
`model_gff` param <br>
2) Specify gff file containing est2genome results (computed using
MAKER2) using the `est_gff` param<br>
3) Specify gff file containing protein2genome results (computed
using MAKER2) using the `protein_gff` param<br>
4) Specify the genome fasta sequence file using the `genome` param<br>
<br>
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:<br>
<big><tt>mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl
maker_bopts.ctl maker_exe.ctl 2>&1 | tee maker.err</tt></big><br>
<br>
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).<br>
<br>
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.<br>
<br>
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.<br>
<br>
What might be the issue?<br>
<br>
Also, apart from this one error, I notice another error:<br>
<big><tt>ERROR: Non-unique top level ID for chr5:hit:1454:4_0<br>
While this is technically legal in GFF3, it usually<br>
indicates a poorly fomatted GFF3 file (perhaps you<br>
tried to merge two GFF3 files without accounting for<br>
unique IDs). MAKER will not handle these correctly.</tt></big><br>
<br>
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?<br>
<br>
Below is my `maker.err` file from the run. (Dropbox link)<br>
<br>
Thank you very much.<br>
Best,<br>
<br>
Vivek<br>
<br>
--<br>
Vivek Krishnakumar<br>
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:vkrishnakumar@jcvi.org">vkrishnakumar@jcvi.org</a><br>
<br>
<div style="padding: 15px; background-color: rgb(217, 237, 255);">
<div style="margin-bottom: 15px;">I've linked 1 file to this
email:</div>
<div style="background-color: rgb(255, 255, 255); padding:
15px;">
<div style="border: 1px solid rgb(205, 205, 205);
border-radius: 5px 5px 5px 5px; margin-top: 10px;
margin-bottom: 10px; padding: 15px;" class="cloudAttachmentItem"><img src="cid:part2.08050703.05020100@jcvi.org" style="margin-right: 5px; float: left; width: 24px;
height: 24px;"><a moz-do-not-send="true" style="color:
rgb(15, 126, 219) ! important;" href="http://db.tt/2tYyKCD7">maker.err</a><span style="margin-left: 5px; font-size: small; color: grey;">(97.7
MB)</span><span style="float: right;"><img style="margin-right: 5px;" src="cid:part4.01000405.03030501@jcvi.org"><a moz-do-not-send="true" style="color: rgb(15, 126, 219) !
important;" href="https://www.dropbox.com/">Dropbox</a></span><a moz-do-not-send="true" style="color: rgb(15, 126, 219) !
important; font-size: small; display: block;" href="http://db.tt/2tYyKCD7">http://db.tt/2tYyKCD7</a></div>
</div>
<div style="color: rgb(68, 68, 68); font-size: small;
margin-top: 15px;"><a moz-do-not-send="true" style="color:
rgb(15, 126, 219) ! important;" href="http://www.getthunderbird.com">Mozilla Thunderbird</a>
makes it easy to share large files over email.</div>
</div>
<br>
</blockquote>
<br>
</div></div>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>