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Update docs/usage.md

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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Sofia Stamouli 2022-09-13 18:13:00 +02:00 committed by GitHub
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@ -415,4 +415,8 @@ NXF_OPTS='-Xms1g -Xmx4g'
### I get a warning during centrifuge_kreport process with exit status 255.
When a sample has no hits, `centrifuge` classifier exits with exit code `255`. The pipeline does not fail and this is provided as a `WARN`.
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.