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. My data structure is shown below. I thought I had to call the program on the
~/Data/Raw Data/170203_NB501802_0007_AH5YHJBGX2$ level, but maybe I'm mistaken. 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 appreciate any advice on how to solve this issue!