From ded6d7ab1f5b595b10cdaf6c5d68b00a30500e18 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 13 Sep 2022 18:13:00 +0200 Subject: [PATCH] Update docs/usage.md Co-authored-by: James A. Fellows Yates --- docs/usage.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index ead0ea2..8ae5257 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -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.