From carsonhh at gmail.com  Thu Feb  2 14:36:27 2023
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 2 Feb 2023 14:36:27 -0700
Subject: [maker-devel] maker error message: DBD::SQLite::db commit
 failed: disk I/O error
In-Reply-To: <CAJXBKVnEDMjK2Az_FupdAFHoWeFyPbrpjvf6oDpbOju7TAUqHw@mail.gmail.com>
References: <CAJXBKVnEDMjK2Az_FupdAFHoWeFyPbrpjvf6oDpbOju7TAUqHw@mail.gmail.com>
Message-ID: <24D15304-2D9C-49BE-B20B-E54B51E4FB2C@gmail.com>

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20230202/2afbb5aa/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20230202/2afbb5aa/attachment-0001.p7s>

From brett.milash at utah.edu  Thu Feb  9 11:13:16 2023
From: brett.milash at utah.edu (Brett A Milash)
Date: Thu, 9 Feb 2023 18:13:16 +0000
Subject: [maker-devel] Ran into unknown state (hex char: 29) at ...
 ../lib/Proc/Signal.pm line 177
Message-ID: <DM6PR11MB3771FC6D9773322B60CB6534E1D99@DM6PR11MB3771.namprd11.prod.outlook.com>

Hi Carson et al. ? I?m trying to install maker 3.01.04 on Rocky Linux 8.5 at the CHPC and am running into this error:


Ran into unknown state (hex char: 29) at /uufs/chpc.utah.edu/sys/installdir/r8/maker/3.01.04/maker/bin/../lib/Proc/Signal.pm line 177.

Any suggestions?
Thanks,
--
Brett Milash
Center for High Performance Computing
University of Utah

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20230209/90441fc8/attachment.html>

From carsonhh at gmail.com  Thu Feb  9 11:25:27 2023
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 9 Feb 2023 11:25:27 -0700
Subject: [maker-devel] Ran into unknown state (hex char: 29) at ...
 ../lib/Proc/Signal.pm line 177
In-Reply-To: <DM6PR11MB3771FC6D9773322B60CB6534E1D99@DM6PR11MB3771.namprd11.prod.outlook.com>
References: <DM6PR11MB3771FC6D9773322B60CB6534E1D99@DM6PR11MB3771.namprd11.prod.outlook.com>
Message-ID: <78C7E6CB-1877-4A4F-9CA7-8F7F03D6FBE2@gmail.com>

Hi Brett,

The specific module is seeing a weird character returned form the system signals table (it happens sometimes). The user can just ignore it and restart (maker will pick back up where it left off). Or they can set '-nolock? on the command line and it won?t even call the module. If doing the latter, make sure to only run MAKER once (can still be an MPI run with multiple CPUs and nodes), but do not start multiple independent MAKER jobs in the same directory simultaneously as file locking will be disabled.

If it?s happening on every run, I can see about editing the module (it is an external Perl module, so I would be doing a custom edit and not use the CPAN version).

Thanks,
Carson



> On Feb 9, 2023, at 11:13 AM, Brett A Milash <brett.milash at utah.edu> wrote:
> 
> Hi Carson et al. ? I?m trying to install maker 3.01.04 on Rocky Linux 8.5 at the CHPC and am running into this error:
>  
> Ran into unknown state (hex char: 29) at /uufs/chpc.utah.edu/sys/installdir/r8/maker/3.01.04/maker/bin/../lib/Proc/Signal.pm <http://chpc.utah.edu/sys/installdir/r8/maker/3.01.04/maker/lib/Proc/Signal.pm> line 177.
>  
> Any suggestions?
> Thanks,
> -- 
> Brett Milash
> Center for High Performance Computing
> University of Utah
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20230209/607630d0/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20230209/607630d0/attachment.p7s>

From carsonhh at gmail.com  Thu Feb  2 14:36:27 2023
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 2 Feb 2023 14:36:27 -0700
Subject: [maker-devel] maker error message: DBD::SQLite::db commit
 failed: disk I/O error
In-Reply-To: <CAJXBKVnEDMjK2Az_FupdAFHoWeFyPbrpjvf6oDpbOju7TAUqHw@mail.gmail.com>
References: <CAJXBKVnEDMjK2Az_FupdAFHoWeFyPbrpjvf6oDpbOju7TAUqHw@mail.gmail.com>
Message-ID: <24D15304-2D9C-49BE-B20B-E54B51E4FB2C@gmail.com>

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20230202/2afbb5aa/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20230202/2afbb5aa/attachment-0002.p7s>

From brett.milash at utah.edu  Thu Feb  9 11:13:16 2023
From: brett.milash at utah.edu (Brett A Milash)
Date: Thu, 9 Feb 2023 18:13:16 +0000
Subject: [maker-devel] Ran into unknown state (hex char: 29) at ...
 ../lib/Proc/Signal.pm line 177
Message-ID: <DM6PR11MB3771FC6D9773322B60CB6534E1D99@DM6PR11MB3771.namprd11.prod.outlook.com>

Hi Carson et al. ? I?m trying to install maker 3.01.04 on Rocky Linux 8.5 at the CHPC and am running into this error:


Ran into unknown state (hex char: 29) at /uufs/chpc.utah.edu/sys/installdir/r8/maker/3.01.04/maker/bin/../lib/Proc/Signal.pm line 177.

Any suggestions?
Thanks,
--
Brett Milash
Center for High Performance Computing
University of Utah

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20230209/90441fc8/attachment-0002.html>

From carsonhh at gmail.com  Thu Feb  9 11:25:27 2023
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 9 Feb 2023 11:25:27 -0700
Subject: [maker-devel] Ran into unknown state (hex char: 29) at ...
 ../lib/Proc/Signal.pm line 177
In-Reply-To: <DM6PR11MB3771FC6D9773322B60CB6534E1D99@DM6PR11MB3771.namprd11.prod.outlook.com>
References: <DM6PR11MB3771FC6D9773322B60CB6534E1D99@DM6PR11MB3771.namprd11.prod.outlook.com>
Message-ID: <78C7E6CB-1877-4A4F-9CA7-8F7F03D6FBE2@gmail.com>

Hi Brett,

The specific module is seeing a weird character returned form the system signals table (it happens sometimes). The user can just ignore it and restart (maker will pick back up where it left off). Or they can set '-nolock? on the command line and it won?t even call the module. If doing the latter, make sure to only run MAKER once (can still be an MPI run with multiple CPUs and nodes), but do not start multiple independent MAKER jobs in the same directory simultaneously as file locking will be disabled.

If it?s happening on every run, I can see about editing the module (it is an external Perl module, so I would be doing a custom edit and not use the CPAN version).

Thanks,
Carson



> On Feb 9, 2023, at 11:13 AM, Brett A Milash <brett.milash at utah.edu> wrote:
> 
> Hi Carson et al. ? I?m trying to install maker 3.01.04 on Rocky Linux 8.5 at the CHPC and am running into this error:
>  
> Ran into unknown state (hex char: 29) at /uufs/chpc.utah.edu/sys/installdir/r8/maker/3.01.04/maker/bin/../lib/Proc/Signal.pm <http://chpc.utah.edu/sys/installdir/r8/maker/3.01.04/maker/lib/Proc/Signal.pm> line 177.
>  
> Any suggestions?
> Thanks,
> -- 
> Brett Milash
> Center for High Performance Computing
> University of Utah
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20230209/607630d0/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20230209/607630d0/attachment-0002.p7s>