brianjohnhaas
commented
5 years ago Hi Atef,
It looks like the file system is having trouble interacting with the sqlite database here for some reason. If you're on a networked file system (NFS), try moving the sqlite database to /tmp, and then using it from there. That could solve the disk I/O issues.
best,
~brian
On Tue, Jun 4, 2019 at 7:02 AM Ahmed Atef notifications@github.com wrote:
Dear Brian, I think Trinotate is a great tool for sequence annotation i would like to thank you for. I have problem when i am trying to import transcript names to Trinotate.sqlite database ( and for every next step when i am trying to build TrinotateWeb). I have very limited knowledge about sqlite. here the error
Trinotate-Trinotate-v3.1.1/util/annotation_importer/ import_transcript_names.pl Trinotate.sqlite Trinotate.xls [42400] DBD::SQLite::db commit failed: disk I/O error at /home/atef/Annotation/Trinotate-Trinotate-v3.1.1/util/annotation_importer/ import_transcript_names.pl line 57, <$fh> line 42401. DBD::SQLite::db commit failed: disk I/O error at /home/atef/Annotation/Trinotate-Trinotate-v3.1.1/util/annotation_importer/ import_transcript_names.pl line 57, <$fh> line 42401.
Atef
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AhmedAtef1231
Dear Brian, I think Trinotate is a great tool for sequence annotation i would like to thank you for. I have problem when i am trying to import transcript names to Trinotate.sqlite database ( and for every next step when i am trying to build TrinotateWeb). I have very limited knowledge about sqlite. here the error
Trinotate-Trinotate-v3.1.1/util/annotation_importer/import_transcript_names.pl Trinotate.sqlite Trinotate.xls [42400] DBD::SQLite::db commit failed: disk I/O error at /home/atef/Annotation/Trinotate-Trinotate-v3.1.1/util/annotation_importer/import_transcript_names.pl line 57, <$fh> line 42401. DBD::SQLite::db commit failed: disk I/O error at /home/atef/Annotation/Trinotate-Trinotate-v3.1.1/util/annotation_importer/import_transcript_names.pl line 57, <$fh> line 42401.
Atef