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

[yuxi hu]

Hi, Carson

I change the TMP directory to an NFS location, but it still gave the same
error message as follows:

STATUS: Parsing control files...

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.

...


Thanks,

Yuxi

Carson Holt <carsonhh at gmail.com> 于2022年12月2日周五 00:34写道：

> Cause is stated in the error message —>
>
> 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.
>
>
> Don’t set TMP= to a network mounted location.
>
> —Carson
>
>
> On Dec 1, 2022, at 4:40 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
>
>
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