Have you checked to make sure the ID that you are using (interactively) is 
permitted read/write access to the directory containing the db files and to the 
files themselves?  I mean *actually* checked that you have permission, since I 
doubt that the CGI process is running with the same ID you are using to logon.

---
The fact that there's a Highway to Hell but only a Stairway to Heaven says a 
lot about anticipated traffic volume.


>-----Original Message-----
>From: sqlite-users [mailto:sqlite-users-
>boun...@mailinglists.sqlite.org] On Behalf Of Luiz Américo
>Sent: Wednesday, 26 September, 2018 20:05
>To: General Discussion of SQLite Database
>Subject: [sqlite] Can write to database using API but get an error on
>writing with sqlite3.exe
>
>I have a 1GB database configured to use WAL mode.
>
>It's accessed by short lived CGI processes, under windows 2008
>server. Each
>process usually opens the database, execute a select or
>update/insert,
>close the connection and finishes. It uses c api
>(sqlite3_open, sqlite3_prepare, sqlite3_step) of dll downloaded from
>sqlite.org.
>
>All operations are working fine (reading, writing to the database).
>Those
>processes are started ~1 to 5 per second
>
>There's a ~5MB wal and shm file that are being updated frequently
>
>When i open the same database with sqlite3.exe (or an external tool
>like
>Sqlite Expert) i can do read commands (select), but when i try to
>write to
>database (UPDATE / ALTER TABLE) it gives a "Attempt to write a read
>only
>database" error.
>
>The tools are executed in the same machine as the datafile
>
>If i try to open a (smaller, less accessed) database in the same
>folder as
>the main one all writing operations are allowed in the external tools
>
>Any hints on what's going on?
>
>Luiz
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