nanoporetech / dorado

Oxford Nanopore's Basecaller

https://nanoporetech.com/

Other

445 stars 54 forks source link

Question on: [warning] Unexpected adapter/primer trim interval #814

Closed osilander closed 1 month ago

osilander commented 1 month ago

Issue Report

Please describe the issue:

We had three warnings thrown after the most recent basecalling (of a few million reads), all along the lines of:

[warning] Unexpected adapter/primer trim interval 36-14 for TGTTATGTCTGGTATTTCGTTCAGTTACGTATTGCTGGCGTCTGCTTGGGTGTTTAACCTTGTTTTAGTTGTTTTAGTTGTTTTAGTTGTTTTAGTTGTTTTAATTGTTTTAGTTGGTTTAGTTGTTTTAGGTTAAACACCGAGCAGGACGCCAGCAATACGTG

When/why are these warnings thrown?

Run environment:

Dorado version: 0.6.0+7a6ab9a
Dorado command: dorado basecaller
Operating system: Linux Ubuntu
Source data type (e.g., pod5 or fast5 - please note we always recommend converting to pod5 for optimal basecalling performance): pod5

Logs

Please provide output trace of dorado (run dorado with -v, or -vv on a small subset)

tijyojwad commented 1 month ago

Hi @osilander - these warnings show up when our adapter trimming algorithm found incorrect bounds for the adapter to be trimmed. We report it as a warning and leave the read unchanged. So your data is fine, but it's useful for debugging to know what happened. e.g. we can check this example sequence to see what's going on