<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>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 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> Kipp Johnson <<a href="mailto:kippjohnson@uchicago.edu">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">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><br></div><span style="color: rgb(34, 34, 34); font-size: 12.666666984558105px; background-color: rgb(255, 255, 255); font-family: arial, sans-serif; ">Hi,</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.666666984558105px;background-color:rgb(255,255,255)"><br style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.666666984558105px;background-color:rgb(255,255,255)"><span style="color: rgb(34, 34, 34); font-size: 12.666666984558105px; background-color: rgb(255, 255, 255); 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-family:arial,sans-serif;font-size:12.666666984558105px;background-color:rgb(255,255,255)"><br style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.666666984558105px;background-color:rgb(255,255,255)"><span style="color: rgb(34, 34, 34); font-size: 12.666666984558105px; background-color: rgb(255, 255, 255); font-family: arial, sans-serif; ">1)</span><br style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.666666984558105px;background-color:rgb(255,255,255)"><br style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.666666984558105px;background-color:rgb(255,255,255)"><span style="color: rgb(34, 34, 34); font-size: 12.666666984558105px; background-color: rgb(255, 255, 255); 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-family:arial,sans-serif;font-size:12.666666984558105px;background-color:rgb(255,255,255)"><br></div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.666666984558105px;background-color:rgb(255,255,255)"><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" target="_blank" style="color:rgb(17,85,204)">kippjohnson@uchicago.edu</a></div></div>
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