Support for processing data in so-called “colorspace”, as produced by the ABI SOLiD sequencer, was removed from Cutadapt versions newer than 1.18.

To process colorspace data, please use Cutadapt 1.18 or earlier. That version also knows how to process .csfasta/.qual file pairs.

See also the colorspace section in the documentation for Cutadapt 1.18.