I’ve been trying to run this line with 16s sequences following DADA2 16S Chemerin Tutorial:
dada2_filter.R -f primer_trimmed_fastqs --truncLen 260,210 --maxN 0 --maxEE 5,8 --truncQ 2 --f_match R1.*fastq.gz.gz --r_match R2.*fastq.gz.gz -t 9
The script seems to work, produces filtered_fastq files but I obtain this Warning message:
In is.na(x[[i]]) :
is.na() applied to non-(list or vector) of type ‘environment’
Creating output directory:filtered_fastqs
Next step in the pipeline requires seqtap.rds file this is missing. Any idea as to why?