Paired-end Cutadapt Produces Empty List

Using cutadapt with a paired collection produces an accurate cutadapt report, with a full list of adapter sequences trimmed; however, the sequence output is an empty list. I selected “Multiple output: create a separate file for each adapter trimmed (default: all trimmed reads are in a single file)” but still only receive an empty list as the output.

Please note that when using cutadapt with a single read file, the report is generated correctly, and the multiple outputs are generated correctly as a list. Is there an optimal way to specify cutadapt paired read inputs to generate the correct output?

Change your tool and then examine the results.
Recommending Trim Galore or Trimmomatic

Unfortunately TrimGalore and Trimmomatic cannot perform the cutadapt function of separating the reads by internal adapter, while retaining the “untrimmed” sequence. cutadapt can accomplish this function easily in a unix/linux environment, but fails on Galaxy.