<div dir="ltr"><font face="arial, sans-serif">Hi, Carson</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">I change the <span style="text-align:justify">TMP directory</span><span class="gmail-Apple-converted-space" style="text-align:justify"> to an NFS location, but it still gave the same error message as follows:<br></span></font></div><div><span class="gmail-Apple-converted-space" style="text-align:justify"><font face="arial, sans-serif"><br></font></span></div><div><span class="gmail-Apple-converted-space" style="text-align:justify"><font face="arial, sans-serif"><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">STATUS: Parsing control files...</span></p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">STATUS: Processing and indexing input FASTA files...</span></p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">STATUS: Setting up database for any GFF3 input...</span></p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">DBD::SQLite::db commit failed: disk I/O error at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 116.</span></p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">DBD::SQLite::db commit failed: disk I/O error at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 310.</span></p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">DBD::SQLite::db do failed: no such table: sources at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 407.</span></p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">DBD::SQLite::db commit failed: disk I/O error at /home/huyxii/software//maker/bin/../lib/GFFDB.pm line 450.</span></p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)">






</p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">DBD::SQLite::db do failed: no such table: sources at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 407.</span></p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)">...</p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)"><br></p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)">Thanks,</p><p style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(0,0,0)">Yuxi</p></font></span></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> 于2022年12月2日周五 00:34写道：<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="auto">Cause is stated in the error message —><br><br><blockquote type="cite"><div dir="ltr"><div dir="ltr"><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">WARNING: Temporary directory set to an NFS location.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">TMP=/home/huyxii/06.annotation/002.gene/06.maker/round1/tmp</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif">The temporary directory in MAKER is specifically for operations that are not NFS-safe, but you have chosen to ignore this error. If you experience seemly random freezing and failures, the TMP directory is the cause.</font></p></div></div></blockquote><div><br></div>Don’t set TMP= to a network mounted location.<div><br></div><div>—Carson</div><div><div><div dir="ltr"><br></div><div dir="ltr"><br><blockquote type="cite">On Dec 1, 2022, at 4:40 AM, yuxi hu <<a href="mailto:yuxihu08@gmail.com" target="_blank">yuxihu08@gmail.com</a>> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="ltr"><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">Hello,</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">I'm trying to use the MAKER pipeline to<span> </span></span><span style="font-size:10.5pt">do genome annotation. When I ran maker for the first time, it ran successfully, but after running for a day, I found this error message: "DBD::SQLite::db disk I/O error." Then I tried to re-run maker, but it didn't seem to work at all. I got error massage like these:</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">STATUS: Parsing control files...</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">WARNING: Temporary directory set to an NFS location.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">TMP=/home/huyxii/06.annotation/002.gene/06.maker/round1/tmp</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">The temporary directory in MAKER is specifically for operations that are not NFS-safe, but you have chosen to ignore this error. If you experience seemly random freezing and failures, the TMP directory is the cause.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">STATUS: Processing and indexing input FASTA files...</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">STATUS: Setting up database for any GFF3 input...</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db commit failed: disk I/O error at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 116.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db commit failed: disk I/O error at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 310.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: sources at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 407.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db commit failed: disk I/O error at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 450.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: sources at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 407.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db commit failed: disk I/O error at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 438, <$IN> line 10004.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10005.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10006.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10007.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10008.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10009.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10010.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10011.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">......</span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><span style="font-family:arial,sans-serif;font-size:10.5pt"><br></span></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><span style="font-family:arial,sans-serif;font-size:10.5pt">The command I use</span><span style="font-family:arial,sans-serif;font-size:10.5pt">d</span><span style="font-family:arial,sans-serif;font-size:10.5pt">: mpiexec -np 56 maker -base Fn maker_bopts.ctl maker_exe.ctl maker_opts.ctl --ignore_nfs_tmp >&2 2>Fn.maker_round1.log</span></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">I have no idea whats going on here. What might be the issue?</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">Thanks in advance for any help.</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><font face="arial, sans-serif"><span style="font-size:10.5pt">Best,</span><span style="font-size:10.5pt"></span></font></p><p class="MsoNormal" style="margin:0pt 0pt 0.0001pt;text-align:justify;font-size:10.5pt;color:rgb(0,0,0)"><span style="font-size:10.5pt"><font face="arial, sans-serif">Yuxi Hu</font></span><font face="Calibri"><span style="font-size:10.5pt"></span></font></p></div>
</div></blockquote></div></div></div></blockquote></div>