Troubleshooting DRAGEN analysis error UMI processing is enabled but QNAME does not have UMI section

DRAGEN can process data from whole genome and hybrid-capture assays with unique molecular identifiers (UMI). UMIs are molecular tags added to DNA fragments before amplification to determine the original input DNA molecule of the amplified fragments. UMIs help reduce errors and biases introduced by DNA damage such as deamination before library prep, PCR error, or sequencing errors.

To use the UMI Pipeline, the input reads files must be from a paired-end run. Input can be pairs of FASTQ files or aligned/unaligned BAM input.

If users encounter this error: "UMI processing is enabled, but QNAME does not have UMI section error", DRAGEN is complaining about missing UMI in the header of the FASTQ file input.

This error means the FASTQ file read name does not include the UMI sequence. However, if UMI option is enabled, DRAGEN expects the UMI in the header of FASTQ file:

The \*.fastq files need to have UMI barcode in 8th field of the read name (QNAME). See the following example.

@NS500561:434:H5LC2BGXJ:1:11101:10798:1359:CACATGA+ACATTC 1:N:0:TGGTACCTAA+AGTACTCATG

For more information about the usage of UMI pipeline in DRAGEN, refer to Unique Molecular Identifiers.

To resolve this issue, users need to regenerate the FASTQ with appropriate settings to include UMI in the header of the FASTQ files. Specifically, users need to use the OverrideCycles setting using BCL Convert ( local tool or BCL Convert app).

The OverrideCycles option tells BCL Convert the location of the UMI bases and how to handle each read. (eg, OverrideCycles, Y101;U20;I8;Y101)

Example how to set up the OverrideCycle option in the Sample Sheet can be found here.

Using Run Planning (link required BaseSpace login) is recommended to generate a sample sheet for reanalysis to make sure that the required fields and formatting are correct.

For any feedback or questions regarding this article (Illumina Knowledge Article #8107), contact Illumina Technical Support [e-mail].