Just a quick comment on this. I spoke with @Sydney_Morgan in person (same uni) regarding her issue. Not sure if this relates to the actual error message she is seeing but from a quick glance it looked to me that her forward and reverse reads fastq files were significantly different in size. I know they don’t have to be exact but they were different by a couple of folds. I suspected that the files may have been transferred incompletely when they were transferred on a FAT32 format USB between computers (4G limit?). So I suggested that she try transferring the files again on an NTSF format and try joining those files before trying demultiplexing them.
Again, not sure if this would deal with that specific error but thought I’d update here anyways in case.
Thanks @Mehrbod_Estaki for the suggestion. I think you are correct in what’s happening.
It looks like the code is trying to strip some trailing whitespace, but it hit an end-of-file in the middle of a fastq record (because of the incomplete transfer).
Keep us posted if re-transferring the data doesn’t fix it!