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When a cron job fails on a VPS, check it in layers: confirm the crontab and owning user, verify the five-field schedule, use absolute command paths and an explicit environment, reproduce the command as that user, confirm the cron service is running, then inspect captured output and system logs. For jobs that must survive downtime, also check for missed-run behavior and duplicate systemd or anacron schedules.
The most common cause is not a broken scheduler. It is a job installed in the wrong user’s crontab, a command that depends on an interactive shell, a service that is disabled after reboot, or a file in /etc/cron.d that violates its syntax or filename rules.
Start with a layered diagnosis
Work from the job definition outward. This prevents you from changing a schedule when the real problem is a missing executable, wrong account, or stopped service.
- List the crontab for the account that should run the job.
- Check every schedule field, the intended timezone, and the command text.
- Replace relative paths with absolute paths and define required environment variables.
- Run the exact command manually as the cron user.
- Check whether
cronorcrondis active and enabled at boot. - Redirect output temporarily and inspect the service journal or syslog.
- If the job is system-wide, validate its file syntax, ownership, permissions, and filename.
- Look for a systemd timer or anacron implementation that duplicates or replaces the cron job.
- Decide whether a missed run after a shutdown should be caught up by a persistent timer or anacron-style scheduler.
1. Confirm the crontab and the account that owns it
Each user has a separate crontab. Debian’s crontab manual states: “Each user has their own crontab, and commands in any given crontab will be executed as the user who owns it.” A line in the application account’s crontab therefore runs with that account’s permissions, home directory, environment, and access to files. A line in root’s crontab does not install the same job for the application account.
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List the intended user’s jobs
crontab -lRun that command while logged in as the account that should execute the task. For a root-owned job, list root’s crontab explicitly:
sudo crontab -lIf you administer several accounts, repeat the check for each one. A frequent failure pattern is editing a user crontab with sudo crontab -e, then expecting an unprivileged application process to see the entry, or editing the application account’s crontab when the command needs root privileges.
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Check where the job is defined
Jobs can come from a per-user crontab, /etc/crontab, files in /etc/cron.d, or scripts in /etc/cron.hourly, /etc/cron.daily, /etc/cron.weekly, and /etc/cron.monthly. These locations are not interchangeable. System-wide crontab formats include an explicit user field; a per-user crontab does not. Open the file you actually intend to use before changing the line.
2. Validate the schedule, timezone, and command text
A standard cron entry has five schedule fields followed by the command:
| Field | Allowed values | Question to ask |
|---|---|---|
| Minute | 0–59 | Is the minute valid, and is it the minute you intended? |
| Hour | 0–23 | Is the VPS using the timezone you assumed? |
| Day of month | 1–31 | Does the date exist in the month? |
| Month | 1–12 or names supported by the implementation | Is the job restricted to the intended months? |
| Day of week | 0–7 or names supported by the implementation | Does the chosen value represent the weekday you expect on this distribution? |
Check the VPS timezone with timedatectl where available, and compare it with the timezone used by your application or operations team. A job scheduled for 02:00 local time may run at a different wall-clock time when the server is configured for UTC. Review daylight-saving changes if the exact local minute matters.
Keep comments and quoting unambiguous
Put comments on their own lines while diagnosing. An inline comment or an unmatched quote can change the command that cron passes to the shell. Shell metacharacters, percent signs, and nested quotes deserve special attention; copy the command into a shell prompt and verify that it parses as intended before putting it back in the crontab.
Use a known-good test schedule temporarily
To distinguish a schedule problem from a command problem, temporarily schedule a harmless test that writes the current time to a file:
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* * * * * /bin/date >> /tmp/cron-heartbeat.log 2>&1Wait several minutes, then inspect the file. Remove the heartbeat entry after testing. If it never appears, investigate the service, the crontab location, and permissions before debugging the original application command.
3. Remove interactive-shell assumptions
Cron does not start your normal interactive login session. Startup files such as .bashrc or shell profile scripts may not run, and the working directory may not be your project directory. Commands that work over SSH can therefore fail immediately under cron.
Use absolute executable paths
Find the executable used by the job and put its full path in the entry. Typical examples are /usr/bin/php and /usr/bin/curl; verify the actual path on your VPS with command -v php or command -v curl.
*/5 * * * * /usr/bin/php /var/www/app/bin/worker.phpDo not rely on a shell alias, a language-version manager loaded only for SSH, or a relative executable name.
Set the environment explicitly
Define a minimal PATH and any variables the command requires. Set the working directory in a wrapper script or change directory explicitly:
SHELL=/bin/sh
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
APP_ENV=production
*/5 * * * * cd /var/www/app && /usr/bin/php bin/worker.phpUse the same configuration file, credentials mechanism, and network endpoint that the application expects, but avoid placing secrets directly in a world-readable crontab. A wrapper script with restricted ownership and mode is usually safer for sensitive values.
Make file locations explicit
Convert paths such as ./storage/output.log or config/settings.yml into absolute paths, or perform an explicit cd first. Cron’s working directory is not guaranteed to be the directory you used during an SSH session. Also confirm that the cron user can traverse every parent directory and write to the destination.
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4. Reproduce the command as the cron user
Run the exact command under the same account, with the same absolute paths, rather than testing it only as root or as your login user:
sudo -u APPUSER -- /absolute/path/to/command --same --argumentsFor a script that expects a project directory, reproduce the directory change too:
sudo -u APPUSER -- sh -c 'cd /var/www/app && /usr/bin/php bin/worker.php'Capture the command’s exit status immediately:
sudo -u APPUSER -- /absolute/path/to/command
printf 'exit status: %sn' "$?"An exit status other than zero confirms an application, permission, dependency, or input failure independent of cron. Fix that failure first. If the command succeeds manually but fails from cron, compare the environment, working directory, umask, network availability, and file permissions between the two executions.
5. Check whether the cron service is running
The scheduler itself must be active. Debian- and Ubuntu-style systems normally use the cron service; Red Hat-style systems commonly use crond.
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Debian or Ubuntu-style commands
systemctl status cron
sudo systemctl enable --now cronRed Hat-style commands
systemctl status crond
sudo systemctl enable --now crondThe first command shows whether the service is running and reports recent failures. The enable --now form starts it immediately and enables it for future boots. If your distribution uses a different unit name, identify the packaged service and use that exact name rather than enabling both variants.
A service can be running now but disabled at boot, which explains jobs that stop after a VPS reboot. Conversely, a failed service may restart repeatedly; inspect its status output and journal before assuming the crontab is at fault.
6. Capture output and inspect logs
Many cron implementations email command output, but VPS images often have no local mail delivery configured. Redirect stdout and stderr while diagnosing so every failure is recorded:
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*/5 * * * * cd /var/www/app && /usr/bin/php bin/worker.php >> /var/log/myjob.log 2>&1Ensure the cron user can create and append to that log. For an unprivileged account, use a writable application log directory instead of /var/log, or create the file with appropriate ownership before testing.
Read the scheduler journal
journalctl -u cron
journalctl -u crondUse the unit that exists on your distribution. To narrow the search, add a time range such as --since "1 hour ago", then look for the command, account, exit status, permission errors, or an indication that the entry was ignored. Traditional installations may also record cron messages in the relevant syslog facility; inspect the system log when the service journal is empty.
Debian documentation also describes journal inspection for generated cron services. On a system using that implementation, the generated service’s journal can contain the command’s actual failure even when the parent scheduler appears healthy.
7. Validate files in /etc/cron.d and /etc/cron.*
System-wide directories have additional rules that do not apply to a user’s crontab.
/etc/cron.d syntax
A line in /etc/cron.d includes the five schedule fields, a username, and then the command:
15 2 * * * appuser /usr/bin/php /var/www/app/bin/cleanup.phpThe username is mandatory in this format. Copying a line directly from crontab -e and omitting that field shifts the command into the wrong columns, so the file may be ignored or behave unexpectedly.
Ownership, mode, and filename characters
Inspect these files with ls -l. Verify the expected owner, restrictive permissions, and any executable-bit requirement documented by your distribution. Debian’s systemd-cron documentation says generated cron filenames must contain only ASCII letters, digits, underscores, or dashes; a name containing a dot, space, or other character can be ignored. Rename an invalid file and then recheck the scheduler journal.
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Periodic directories and run-parts
Hourly, daily, weekly, and monthly directories are commonly processed by run-parts. Red Hat documentation describes that mechanism. A script with an unsupported filename, incorrect mode, missing interpreter, or nonfunctional shebang may be skipped or fail when the directory is scanned. Test the script directly as its intended user, and use a simple filename containing only letters, digits, underscores, or dashes.
8. Investigate reboot and shutdown gaps
A normal cron schedule is evaluated at its scheduled minutes. If the VPS is powered off at that minute, cron does not automatically replay the missed invocation when the machine returns. This is expected behavior, not evidence that the entry disappeared.
Choose the required guarantee
- If an occasional missed run is acceptable, keep cron and document the behavior.
- If a periodic task should run after downtime, use an anacron-style strategy appropriate to your distribution or a persistent systemd timer.
- If the job must run once at an exact wall-clock time, design an explicit recovery or reconciliation step; do not assume ordinary cron provides it.
Debian warns against running duplicate cron and anacron or systemd-cron implementations for the same task because both schedulers can execute the job. Pick one owner for each job and remove or disable the competing entry.
9. Check for systemd timers that replace or duplicate cron
On Debian installations using systemd-cron, crontabs can be translated into generated .timer and .service units. A native timer with a matching name can override a legacy-generated job. This can make a crontab appear correct while a different unit controls the actual execution.
Inventory every timer
systemctl list-timers --allLook for a timer whose schedule or description matches the cron entry. Inspect its status and generated units before creating a replacement:
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systemctl cat NAME.timer
systemctl cat NAME.serviceRead the corresponding journal entries and compare the service’s user, working directory, environment, and command with the old cron definition. Disable one schedule before enabling another; do not leave both active while testing.
Cron or a systemd timer: which should run this job?
| Decision factor | Cron | Systemd timer |
|---|---|---|
| Observability | Entries are simple and logs usually appear in syslog or the cron service journal. | Each run has a unit status and a dedicated journal, making failures and last-run state easier to inspect. |
| Missed-run persistence | Ordinary cron does not catch up after the VPS is off. | A suitably configured persistent timer can trigger after downtime. |
| Dependency ordering | Requires shell-level checks or wrapper logic. | Can express ordering and relationships with other systemd units. |
| Environment isolation | Requires explicit paths, variables, and directory handling in the entry or wrapper. | Environment, user, working directory, and resource controls can be declared in the service unit. |
| Portability | Available across a wide range of Unix-like systems and VPS distributions. | Best suited to a VPS already managed by systemd; not portable to non-systemd hosts. |
| Duplicate-execution risk | Can coexist accidentally with anacron or generated systemd jobs. | Can coexist accidentally with the original cron entry; inventory existing timers first. |
Use cron for a straightforward, portable schedule when exact catch-up and unit dependencies are not required. Prefer a native systemd timer when the VPS is systemd-based and you need persistent missed-run handling, clear journal visibility, dependency ordering, or a tightly controlled service environment. Whichever you choose, maintain one authoritative schedule for the job.
A practical repair example
Suppose a PHP worker runs over SSH but not from cron. Apply the checks in this order:
- As the application account, run
crontab -land confirm the entry is in the correct user’s crontab. - Replace a line such as
*/5 * * * * php bin/worker.phpwith an explicit directory and executable path:*/5 * * * * cd /var/www/app && /usr/bin/php bin/worker.php. - Run
sudo -u appuser -- sh -c 'cd /var/www/app && /usr/bin/php bin/worker.php'and record the exit status. - Check
systemctl status cronorsystemctl status crond, then enable the service at boot if necessary. - Append
>> /var/log/myjob.log 2>&1temporarily, using a log path writable byappuser. - Inspect the relevant journal and application log for missing extensions, denied files, invalid configuration, or network errors.
- Run
systemctl list-timers --allto ensure a generated or native timer is not replacing the crontab or running the worker a second time.
Once the cause is fixed, remove temporary heartbeat and verbose redirection entries if they are no longer needed, but retain a durable logging path and a documented owner for the schedule.
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Common symptoms and the fastest check
| Symptom | Most useful first check |
|---|---|
| Nothing runs and there is no log | List the intended user’s crontab, then check the cron service status. |
| It works in SSH only | Use absolute paths, set PATH, set the working directory, and run as the cron user. |
| It stopped after reboot | Check whether cron or crond is enabled and running. |
The entry is in /etc/cron.d but never fires |
Verify the username field, ownership, mode, and filename characters. |
| The job runs twice | Compare the crontab with systemctl list-timers --all and anacron or periodic-directory entries. |
| A run is missing after an outage | Confirm whether ordinary cron was offline at the scheduled minute; select a persistent timer or anacron-style catch-up if required. |
Final checks before declaring the VPS fixed
- The entry is in the crontab or system file owned by the intended account.
- The schedule matches the VPS timezone and has no malformed fields or inline-comment surprises.
- The command uses absolute paths, an explicit working directory, and all required environment values.
- The command succeeds when run with
sudo -uas the cron user. - The correct scheduler service is running and enabled for boot.
- Output and exit failures are visible in a writable log and in the relevant journal or syslog.
- System-wide files satisfy their username, ownership, mode, executable, and filename rules.
- Only one scheduler owns the job, unless deliberate coordination prevents duplicate execution.
- Missed-run behavior matches the business requirement.
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