From carsonhh at gmail.com Thu Dec 1 09:34:07 2022 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 1 Dec 2022 09:34:07 -0700 Subject: [maker-devel] maker error message: DBD::SQLite::db commit failed: disk I/O error In-Reply-To: References: Message-ID: 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 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuxihu08 at gmail.com Thu Dec 1 04:40:24 2022 From: yuxihu08 at gmail.com (yuxi hu) Date: Thu, 01 Dec 2022 11:40:24 -0000 Subject: [maker-devel] maker error message: DBD::SQLite::db commit failed: disk I/O error Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuxihu08 at gmail.com Fri Dec 2 02:13:03 2022 From: yuxihu08 at gmail.com (yuxi hu) Date: Fri, 02 Dec 2022 09:13:03 -0000 Subject: [maker-devel] maker error message: DBD::SQLite::db commit failed: disk I/O error In-Reply-To: References:

Message-ID: 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 ?2022?12?2??? 00:34??? > 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 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Dec 1 09:34:07 2022 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 1 Dec 2022 09:34:07 -0700 Subject: [maker-devel] maker error message: DBD::SQLite::db commit failed: disk I/O error In-Reply-To: References: Message-ID: 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 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuxihu08 at gmail.com Thu Dec 1 04:40:24 2022 From: yuxihu08 at gmail.com (yuxi hu) Date: Thu, 01 Dec 2022 11:40:24 -0000 Subject: [maker-devel] maker error message: DBD::SQLite::db commit failed: disk I/O error Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuxihu08 at gmail.com Fri Dec 2 02:13:03 2022 From: yuxihu08 at gmail.com (yuxi hu) Date: Fri, 02 Dec 2022 09:13:03 -0000 Subject: [maker-devel] maker error message: DBD::SQLite::db commit failed: disk I/O error In-Reply-To: References: