Yes, This is the bug: Cutadapt thinks my fastq.gz files aren't fastq.gz.
I tried to run it again today and the process actually finished without this bug.
But it didn’t managed to cut my primers, maybe because i am not using the plugin correctly?
This is my primers:
My forward primer is: (ITS86F) - GTGAATCATCGAATCTTTGAA
My reverse primer is : (ITS4) - TCCTCCGCTTATTGATATGC
Since im working with ITS2 - in some of my reads there is a chance my sequence include the reverse complementary primer on the 3’ strand and subsequent bases. So in order to remove them as well i want to ask Cutadapt the following:
On the forward reads remove: forward primer + reverse complementary of the reverse primer.
On the reverse reads remove: reverse primer + reverse complementary of the forward primer.
This is what i ran in the command line:
i also uploaded the qzv of rep-seqs - as you can see in 9 out of 60 samples the Reverse complementary of the ITS4 primer wasn’t removed.
lastly, i uploaded the filtering stats, i am losing most of my data even though i trimmed by quality up until the mean was above 20.
rep-seqs.qzv (212.9 KB)
stats-dada2.qzv (1.2 MB)