[maker-devel] maker error message: DBD::SQLite::db commit failed: disk I/O error

[Carson Holt]

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.

—Carson


> On Dec 1, 2022, at 4:39 AM, yuxi hu <yuxihu08 at gmail.com> wrote:
> 
> Hello,
>  
> I'm trying to use the MAKER pipeline to 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:
>  
> STATUS: Parsing control files...
> WARNING: Temporary directory set to an NFS location.
> TMP=/home/huyxii/06.annotation/002.gene/06.maker/round1/tmp
> 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.
>  
> STATUS: Processing and indexing input FASTA files...
> STATUS: Setting up database for any GFF3 input...
> DBD::SQLite::db commit failed: disk I/O error at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 116.
> DBD::SQLite::db commit failed: disk I/O error at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 310.
> DBD::SQLite::db do failed: no such table: sources at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 407.
> DBD::SQLite::db commit failed: disk I/O error at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 450.
> DBD::SQLite::db do failed: no such table: sources at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 407.
> DBD::SQLite::db commit failed: disk I/O error at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 438, <$IN> line 10004.
> DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10005.
> DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10006.
> DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10007.
> DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10008.
> DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10009.
> DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10010.
> DBD::SQLite::db do failed: no such table: est_gff at /home/huyxii/software/maker/bin/../lib/GFFDB.pm line 496, <$IN> line 10011.
> ......
> 
> The command I used: mpiexec -np 56 maker -base Fn maker_bopts.ctl maker_exe.ctl maker_opts.ctl --ignore_nfs_tmp >&2 2>Fn.maker_round1.log
>  
> I have no idea whats going on here. What might be the issue?
>  
> Thanks in advance for any help.
>  
> Best,
> Yuxi Hu
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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