Nothing to report, or the check does not apply to this input route.
Continue.
Exit 0
WARNING
An advisory finding that may limit interpretation.
Review it, then continue.
Exit 0
REVIEW_REQUIRED
A finding that needs your judgement before you rely on the result.
Tick I reviewed the phase checks marked Review required, then continue.
Exit 0
FAIL
A condition that prevents a correct analysis.
Start is disabled until the named cause is resolved and validation is repeated.
Exit 4
STALE
The saved input validation no longer matches the current configuration, sample sheet or inputs.
Start is disabled until you validate again.
Not reported: only the interface tracks it.
The overall status is the most severe finding, in the order FAIL, REVIEW_REQUIRED, WARNING, PASS; in the interface STALE ranks above FAIL. A workflow already running stops for a FAIL in check 00, project setup; anything but PASS in check 05, reference validation, on FASTQ and SRA routes; or a failed microarray import recorded in checks 11 and 12. Meta-analysis also requires a valid check 01 at PASS or WARNING before its per-study fit; REVIEW_REQUIRED, FAIL, missing or malformed evidence stops that route. Other checks record their status for review in Pre-run checks or results/reports/sanity_checks.txt. Pre-run and result checks says what each numbered check tests.
Success. For check, also when the worst finding is WARNING or REVIEW_REQUIRED.
Read the findings: exit 0 does not mean nothing needs review.
1
An unexpected error, printed with a Python traceback.
Report it with the traceback and the command you ran.
2
A usage error: no command given, or an invalid option or value.
Run bulkseq --help or bulkseq COMMAND --help.
3
The path is not a project; config/config.yaml cannot be read or does not validate; samples show finds no readable sample sheet; or run could not refresh the project’s copy of the workflow.
Check the path given to -C. The message names the configuration field or the workflow problem.
4
check found a FAIL, or the sample sheet is missing or unreadable.
Fix what the FAIL names, then run check again.
5
The workflow run failed, including a failure the WSL launcher reported as success.
Read the log: the first Error in rule line names the failed step.
130
Interrupted with Ctrl-C. The process tree is sent TERM, given up to eight seconds to release its lock, then sent KILL.
Continue with bulkseq run --mode resume.
bulkseq --help prints the same list, built from the constants the command returns, so the two cannot disagree. The command-line page covers running and resuming.
Check Environment writes the installer’s result to Show details / log, for example WSL bioinformatics installer finished with exit code 3.
Exit
Meaning
What to do
0
Installed and verified.
Nothing.
1
The platform is unsupported (the pipeline needs Linux on x86_64 or aarch64, natively or in WSL2); creating the environment failed from both the pinned lock and the floating specification; or verification still failed after the one automatic repair.
Read the last lines of the setup log: they name the failing step, package or probe.
2
An invalid setup argument: a profile other than core or full, or BULKSEQ_REBUILD other than 0 or 1.
Only reachable when the script is run by hand. Run it again with a valid value.
3
The package manager could not be installed: its download failed, or the Linux system has no python3 and no downloader.
Follow the ACTION REQUIRED lines in the log, then click Install / repair core environment again.
4
Another setup held the install lock for more than 30 minutes.
Make sure no other setup is running, then try again.
Read the log: the first Error in rule line names the failed step.
Failed — a rule reported an error (see the log)
A step failed although the launcher returned 0, which the WSL launcher can do. The monitor reads the log to catch it.
As above.
Stopped
You stopped the run. It is marked with a WARNING status.
Resume continues from the completed steps.
When the log shows R or Bioconductor packages failing to load, with there is no package called, will not load in the bulkseq env or unable to load shared object, the monitor offers to rebuild the analysis environment from its pinned lock. The command line reports the same failure as exit 5 and makes no offer.