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

[yuxi hu]

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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