A Mirth Connect File Reader that silently skips files usually comes down to a file mask that doesn't match real filenames, a minimum age or size filter excluding valid files, insufficient permissions on the source directory, or a file still being written when Mirth polls. Fix it by correcting the file pattern against real filenames, adjusting the age or size filter to match how the sender actually writes files, granting the Mirth service account explicit read access, and having the sender write to a temp file and rename it once complete. Prevent recurrence with a standardized filename convention, atomic write patterns, and monitoring the directory for files older than expected.
Quick answer
A Mirth Connect File Reader not picking up files situation is quiet by design — there's usually no exception in the log, just files accumulating in the source directory while the connector reports as running normally. This makes it one of the harder Mirth issues to diagnose, since the connector isn't failing, it's simply not matching files that are there.
Below is what actually causes a File Reader to skip valid files, the fix for each cause, and how to catch it before a directory fills up. Our free Mirth Health Check can check your configuration against what's actually there — part of the Mirth Connect support work we do for US healthcare teams.
What Causes a File Reader to Skip Files?
A File Reader only picks up files that match its configured pattern, age, size, and permission requirements, and any mismatch between that configuration and the real files in the directory produces the same quiet symptom of files simply being ignored entirely.
File Mask Not Matching the Actual Filenames
If the connector's file pattern expects a specific extension or naming format and the actual incoming files don't match it exactly, they'll sit in the directory indefinitely without triggering any error. Case sensitivity is a common, easy-to-miss culprit.
Minimum File Age or Size Filter Excluding Valid Files
A minimum file age setting, intended to avoid picking up files still being written, can also exclude genuinely complete files if the sending system writes them faster or slower than the filter was originally tuned for.
Insufficient Permissions on the Source Directory
If the account Mirth runs as doesn't have read access to the directory or the specific files within it, the File Reader silently can't see them, producing the same symptom as a mismatched file pattern from the outside.
File Still Being Written When Mirth Polls
If the sending system writes a file gradually rather than atomically, Mirth's poll can catch it mid-write, and depending on configuration, either skip it or read an incomplete file before the sender finishes.
How to Fix a File Reader Not Picking Up Files
Start by carefully comparing the connector's exact configured pattern and filters against the real filenames and timestamps sitting in the directory right now, rather than assuming the connector itself is fundamentally broken.
Correct the File Pattern to Match Real Filenames
Update the File Reader's file mask to exactly match the real naming convention in use, including case, and test it against a sample of actual filenames rather than a filename you expect to see.
Adjust the Minimum Age or Size Setting
Loosen or tighten the minimum file age or size filter based on how the sending system genuinely writes files, rather than a generic default that may not fit this particular integration's timing.
Fix Directory Permissions for the Mirth Service Account
Grant the account Mirth runs as explicit read access to the source directory and its files, and verify this directly rather than assuming existing permissions carry over correctly after a server or account change.
Have the Sender Write to a Temp File and Rename
Where possible, have the sending system write to a temporary filename and rename it to its final name only once writing is complete, so Mirth never polls a file that's still being written.
How to Prevent This From Happening Again
Since this failure mode produces no error at all, prevention depends entirely on catching a growing backlog of unprocessed files before anyone notices a downstream gap in the data days or weeks later.
Standardize Incoming Filename Conventions
Agree on an explicit, documented filename pattern with every sending system, and configure the File Reader's mask to match that exact convention rather than a broad pattern that happens to work today.
Use Atomic Write Patterns for Incoming Files
Encourage or require senders to use a write-then-rename pattern for every file drop, which eliminates the partial-write problem entirely regardless of how large or slow the file transfer itself is.
Monitor the Directory for Files Older Than Expected
Set up a simple check that flags any file in the source directory older than your normal processing window, independent of Mirth's own connector status, to catch a silent mismatch quickly.
Alert When Files Accumulate Without Being Picked Up
Combine a file count or age check with an alert so a growing backlog surfaces to a person within hours, rather than being discovered only when someone downstream asks where their data went.
When to call for help
If you've confirmed the file mask and permissions and files are still sitting untouched, the cause is often a subtle timing mismatch between the sender's write pattern and Mirth's minimum age filter. Our free Mirth Connect health checkchecks your configuration against what's actually there as part of the standard diagnostic.
Have an error accompanying it? Send us the log, or check pricing for ongoing support plans.
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