Errors Problems during the analysis

Several errors were encountered throughout the DADA2 pipeline. The solution to each issue is provided with the explanation and a link to the source of the solution.

• Quality Check

plotQualityProfile(fnFs1) Error in density.default(qscore) : 'x' contains missing values

The possible explanation for this error is length zero sequences in the fastq file introduced during the primer clipping steps with cutadapt. This issue can be solved by enforcing a minimum length using cutadapt with the --minimum-length N flag. source