Hi all, back here with another AVITI issue. Our latest AVITI 16S V4 dataset fails at the DADA2 step with the following error:
in dada(drpR, err = errR, multithread = multithread, verbose = FALSE) :
Invalid derep$quals matrix. Quality values must be positive integers.
2: stop("Invalid derep$quals matrix. Quality values must be positive integers.")
1: dada(drpR, err = errR, multithread = multithread, verbose = FALSE)
Has anyone encountered this error? I know a bunch of others have posted here about this error code, but each one has a different cause (1, 2, 3), and I think my cause is different as well.
My guess is DADA2 was built for Illumina data, where the max Qscore is 41. AVITI has higher quality scores (up to Q50; ref). That confuses DADA2's automatic Quality score encoding identifier and misidentifies the data as Phred64 instead of Phred33. To circumvent this, I need to specify to DADA2 that the encoding is strictly Phred33 using the argument: qualityType="FastqQuality" per this thread.
But if I am not mistaken, QIIME2's implementation of DADA2 does not have an option to allow this argument to be passed. Does anyone have any options other than using DADA2 outside of the QIIME2 environment to get past this?
Is there a way to verify if this indeed is the issue, given that this error has been spotted with different causes?
Alternative causes for this error, and troubleshooting steps are welcome.
Thanks in advance for helping out.