Import multiplexed R1.fastq and R2.fastq with mixed forward and reverse reads + truncate reverse primer

Hi there,

I am very excited to see that qiime2 2017/12 includes a new feature to trim forward and reverse primers. Apparently, you were quite busy during Christmas.

I was testing the preliminary q2-cutadapt tutorial, which works fine :+1:

Now I wanted to trim the forward primer from my demultiplexed sequences using "qiime cutadapt trim-single", however, this did not worked so far. I used to following command:

qiime cutadapt trim-single
--i-demultiplexed-sequences DemuxSeq.qza
--p-cores 4
--p-front CCTACGGGNGGCWGCAG
--p-match-read-wildcards
--p-match-adapter-wildcards
--p-error-rate 0
--o-trimmed-sequences trimmed-seqs.qza
--verbose \

The command does not return any error, it is simply running forever. However, the CPU is idle and no memory is used. I stopped it after a while with ctrl + c.

In the following you see a screenshot, showing the first bases of my sequences (including forward primer: CCTACGGGNGGCWGCAG) in fastq format.

Well... its open for discussion and suggestions :slight_smile: