diff --git a/docs/usage.md b/docs/usage.md index 3971c58..8ae5257 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -410,3 +410,13 @@ We recommend adding the following line to your environment to limit this (typica ```bash NXF_OPTS='-Xms1g -Xmx4g' ``` + +## Troubleshooting and FAQs + +### I get a warning during centrifuge_kreport process with exit status 255. + +When a sample has insufficient hits for abundance estimation, the resulting `report.txt` file will be empty. + +When trying to convert this to a kraken-style report, the conversion tool will exit with a status code `255`, and provide a `WARN`. + +This is **not** an error nor a failure of the pipeline, just your sample has no hits to the provided database when using centrifuge.