shane hogle

Spent like the last hour dealing with nearly the same cryptic error message, and I think it has to do with the parsing of fastq headers for the removal of optical duplicates. from the manual... optical=f If true, mark or remove optical duplicates only. This means they are Illumina reads within a certain distance on the flowcell. Normal Illumina names needed. Also for tile-edge and well duplicates. I was trying to remove duplicates in an ncbi SRA download that didn't have the original illumina header...