Thanks @hosismas,
Do you know if other amplicon types were sequenced along with the V4V5 primers? I find it awfully suspicious that consistently ~50% of the R1 and R2 reads have the primers trimmed.
FYI, if you only want to trim adapters you'd need to do so like this:
qiime cutadapt trim-paired
--i-demultiplexed-sequences "$QIIME5_DIR/demux.qza"
--p-adapter-f "$ILLUMINA_FWD_ADAPTER"
--p-adapter-r "$ILLUMINA_REV_ADAPTER"
--p-cores 8
--o-trimmed-sequences "$TRIMMED5_DIR/trimmed_demux.qza \
--verbose"
Here again, even regardless of using both primers & adapters, that only 45-50% of the reads are trimmed. This makes me think there is another amplicon with different primers contained within this run. Do you know if this is true?
If so, then I highly recommend that you make use of the --p-discard-untrimmed. This way you are only writing out reads that are from the targeted amplicon. See here.