Cannot specify ' with failed reads' with cbcl input data." error in bcl2fastq2

Error Message:

Cannot specify '--with-failed-reads' with cbcl input data. Failed reads are not stored in cbcl files.

Root Cause:

NovaSeq 6000, NextSeq 1000/2000 use Real Time Analysis (RTA3) and creates CBCL files. Failed reads are not saved and, therefore, cannot be recovered by using "--with failed-reads".

Solution:

This option cannot be applied to CBCL files. Information is indicated in bcl2fastq2 user guide.

More information about this option:

--with-failed-reads option in bcl2fastq2 includes all clusters in the output, including those that did not pass filter. By default, clusters that did not pass filter are excluded. FASTQ files containing failed reads cannot be uploaded to BaseSpace Sequence Hub.

After cycle 25, RTA2 stops reading clusters that do not pass filter. Systems other than MiSeq and HiSeq 2500 produce 25 bases, then all Ns. This option cannot be applied to CBCL files.

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