FAQ

How do I process MPXV data?

A set of resources for processing MPXV sequencing data may be found here, including running this pipeline on the command line and via the artic MPXV Nextflow pipelines in epi2me.

Where can I find the SOP for SARS-CoV-2?

The standard operating procedure for the ARTIC Network SARS-CoV-2 bioinformatics can be found here.

The pipeline exited with an error code — what does it mean?

See Troubleshooting for a full description of exit codes. Common ones:

• Exit 2 — no reads aligned to the reference. Check that --scheme-name/--scheme-version match your data.
• Exit 3 — primer scheme BED file could not be parsed. The error message will describe the specific failure.
• Exit 6 — Clair3 model selection failed. Use --model to specify a model explicitly (see Clair3 Models).
• Exit 137 — out of memory. Try enabling --normalise or downsampling your source FASTQ files.

I am using Dorado-basecalled reads but the pipeline fails with a model error

The pipeline reads the basecall_model_version_id tag from the first read header to select a Clair3 model automatically. If the tag is present but no compatible Clair3 model exists, the pipeline will exit with code 6.

A common cause is data basecalled with Dorado fast mode: no versioned Clair3 fast models exist for R10.4.1 data. Re-basecall with hac or sup, we do not provide these models so have no control over which ones exist.