I need to preprocess my data with bcl2fastq. Unfortunately, no matter how I try it, I get a "Segmentation Fault" error.
I call bcl2fastq with the command bcl2fastq --no-lane-splitting --mask-short-adapter-reads=13. I thought I had to call the program on the ~/Data/Raw Data/170203_NB501802_0007_AH5YHJBGX2 level, but maybe I'm mistaken. For explanation, in this folder are "Images", "InterOp", and "Data>Intensities>[locs for each line a separate folder] & [basecall folder]".
However, I'll get the same error if I try to call bcl2fastq on another level. If I try to define the input directory with the --input-dir, I'll get the error: Failed to parse the options: too many positional options have been specified on the command line. I would appreciate any advice on how to solve this issue!