reads.fa ids do not have the correct format

it must have the id line >SSS_INT_xINT

SSS is a three letter code indicating the sample origin
INT is just a running number
xINT is the number of read occurrences



You can use the mapper.pl module to create such a file from a fasta file with 
mapper.pl reads.fa -c -m -s reads.fa.collapsed

See also the mapper.pl help for more information on preprocessing input files.