This won't be an issue in the live database, but it happened to me while I was running against my test database. If the join in 1_download_files_and_generate_report.pl between Lab_MiSeq_Run and MiSeqQC_RunParameters only finds one match, then you get this error:
Error in `colnames<-`(`*tmp*`, value = ".FLAG") :
attempt to set 'colnames' on an object with less than two dimensions
A little bit of searching makes it sound like this is a confusion between a vector and a matrix or a data frame.
This can also be caused by the join problems described in issue #20.