dada2: plotQualityProfile - Error: IncompleteFinalRecord

Question

[ben.tatton]

Hi All,

I'm relatively new to analysis on genomic data and I have run up against a wall. I have recently got some pair-end reads back that were sequenced on a Novaseq platform. I have removed the adaptors and done some quality control using fastp on the raw reads. My data was already demultiplexed on receiving it but still had the barcodes and primers attached as part of the "Raw Reads" file. I began the dada2 1.16 tutorial but have ended up bumping up against a wall with the plotQualityProfile function returning an "FastqSampler yield() incomplete final record: c:myfilepath" waring. I've had a look around some of the usual forums which dig me out of holes but they're to no avail this time.

path <- ("C:\\myfilepath")

list.files(path)

fnFs <- sort(list.files(path, pattern= ".raw_1.fq.gz", full.names = T, recursive = T))

fnRs <- sort(list.files(path, pattern= ".raw_2.fq.gz", full.names = T, recursive = T))
####
sample.names <- sapply(strsplit(basename(fnFs), "_"), `[`, 1)
sample.names

fqcprofile <- plotQualityProfile(fnFs[1:13])

> fqcprofile <- plotQualityProfile(fnFs[1:13])
Warning message:
IncompleteFinalRecord
  FastqSampler yield() incomplete final record:
  C:\myfilepath\out.M.raw_1.fq.gz 

[ben.tatton]

To anyone who may find it useful this issue was resolved by uninstalling and reinstalling dada2.