<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">You set TMP= in the maker control file to an NFS location. This creates IO issues. You must set it to a locatl disk location for the machine running maker. Usually best not to set TMP= and just let it use the default /tmp which is almost always local disk.<div><br></div><div>—Carson</div><div><br><div><br><blockquote type="cite"><div>On Dec 1, 2022, at 4:39 AM, yuxi hu <yuxihu08@gmail.com> wrote:</div><br class="Apple-interchange-newline"><div><div dir="ltr"><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><font face="arial, sans-serif"><span style="font-size:10.5pt">Hello,</span><span style="font-size:10.5pt"></span></font></div><p class="MsoNormal" style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><font face="arial, sans-serif"><span style="font-size:10.5pt">I'm trying to use the MAKER pipeline to<span class="gmail-Apple-converted-space"> </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></div><p class="MsoNormal" style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><font face="arial, sans-serif"><span style="font-size:10.5pt">STATUS: Parsing control files...</span><span style="font-size:10.5pt"></span></font></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><p class="MsoNormal" style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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, <$IN> line 10004.</span><span style="font-size:10.5pt"></span></font></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10005.</span><span style="font-size:10.5pt"></span></font></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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, <$IN> line 10006.</span><span style="font-size:10.5pt"></span></font></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10007.</span><span style="font-size:10.5pt"></span></font></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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, <$IN> line 10008.</span><span style="font-size:10.5pt"></span></font></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10009.</span><span style="font-size:10.5pt"></span></font></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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, <$IN> line 10010.</span><span style="font-size:10.5pt"></span></font></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><font face="arial, sans-serif"><span style="font-size:10.5pt">DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10011.</span><span style="font-size:10.5pt"></span></font></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><font face="arial, sans-serif"><span style="font-size:10.5pt">......</span></font></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><span style="font-family:arial,sans-serif;font-size:10.5pt"><br></span></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><p class="MsoNormal" style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><p class="MsoNormal" style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div><p class="MsoNormal" style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><span style="font-size:10.5pt"><font face="arial, sans-serif"> </font></span></p><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><font face="arial, sans-serif"><span style="font-size:10.5pt">Best,</span><span style="font-size:10.5pt"></span></font></div><div style="margin: 0pt 0pt 0.0001pt; text-align: justify; font-size: 10.5pt;"><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></div></div>
_______________________________________________<br>maker-devel mailing list<br>maker-devel@yandell-lab.org<br>http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org<br></div></blockquote></div><br></div></body></html>