It does happen if I start in a different directory. My current working directory is NFS. I changed the tmp directory in maker_opts from the NFS to a local partition (tmpfs), and I'm still getting this error. Does the working directory also have to be locally mounted?<br>
<br><div class="gmail_quote">On Fri, Aug 3, 2012 at 8:27 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>It means that your GFF3 results will not be integrated. Does it happen if you start in a different directory?</div><div><br></div><div>
The lock error is coming from SQLite, and may be the result of your working directory being mounted on an NFS filesystem which is a known issue with SQLite. If you give maker a location for TMP that is not NFS mounted (I.e. A locally mounted filesystem), then maker will try and move the SQLite database off of the NFS mount.</div>
<div><br></div><div>You can check the mount status of the current working directory and the directory you choose fro TMP by using the Linux df command.</div><div><br></div><div>df <directory></div><div><br></div><div>
Any NFS mount will follow the format of host:/location.</div><div><br></div><div>Example:</div><div>152.234.123.234:/data/research</div><div><br></div><div>Or </div><div><br></div><div>storage.utah.edu:/data/research</div>
<div><br></div><div>If you are not running on an NFS device let me know if running in a different directory results in the same error.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Kipp Johnson <<a href="mailto:kippjohnson@uchicago.edu" target="_blank">kippjohnson@uchicago.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, 2 August, 2012 3:12 PM<br>
<span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] "DBD::SQLite::db locked" error; MPICH2 help<br>
</div><div><div class="h5"><div><br></div><span style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif">Hi,</span><br style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif">
<br style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif"><span style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif"> I am running Maker version 2.26. I have two questions:</span><br style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif">
<br style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif"><span style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif">1)</span><br style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif">
<br style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif"><span style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif"> When I run maker, I get errors like the following printed to STDOUT: </span><div style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif">
<br></div><div style="color:rgb(34,34,34);font-size:12.666666984558105px;font-family:arial,sans-serif"><div>DBD::SQLite::db selectcol_arrayref failed: database is locked at /home/zjiang/.mnt/kwj/maker/bin/../lib/GFFDB.pm line 107.</div>
<div>...</div><div>DBD::SQLite::db do failed: database is locked at /home/zjiang/.mnt/kwj/maker/bin/../lib/GFFDB.pm line 109.</div><div>...</div><div>DBD::SQLite::db do failed: database is locked at /home/zjiang/.mnt/kwj/maker/bin/../lib/GFFDB.pm line 497, <$IN> line 2.</div>
<div><br></div><div> I reinstalled the indicated module via cpanm and restarted Maker from the beginning in a new directory, and I am getting the same error. The first time I ran maker, I ignored these and the maker run seemingly proceeded to the process the contigs correctly. Is this something I should be worried about?<br>
<br><br>2)<br><br> I am running Maker on a single server with 64 processors. Would it be faster to use MPICH2, or to simply restart Maker in the same directory ~16 times, with the # of CPUs option that gets passed to Blast set to 4 for each restart?<br>
<br> I believe that I have MPICH2 correctly compiled and installed; if it would be faster to use MPICH2, could someone provide me with a sample command line entry to use for Maker? I am confused about how to run MPICH2 on a single node (without a hostfile?), and searching the maker-dev-list archive seems to give me results for older versions of MAKER and MPICH2.<br>
<br>Thank you,<br><br><br>Best,<br><br> Kipp Johnson<br> <a href="mailto:kippjohnson@uchicago.edu" style="color:rgb(17,85,204)" target="_blank">kippjohnson@uchicago.edu</a></div></div></div></div><div class="im">
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