Hi,
is it possible that the make.fastq will create fastq files with wrapped/multiline sequence and quality scores information.
I fed the make.fastq file with uniline fasta and quality files 13249440 lines each - means i should get 2*13249440=26498880 fastq file
but instead I got a 26498930 line fastq - it seems to have gained 50 extra lines and is not even divisible by 4.
That seems odd. Could you outline the steps you took to determine the difference?