cat all_mapped.fastq | paste - - - - | sed 's/^@/>/g'| cut -f1-2 | tr '\t' '\n' > file_out
time ./cd-hit -i file_out -o otput_cd_hit -M 8000 -T 3

then you go and examine each cluster with something like:

   for i in *.clstr; do \
    echo -n $(echo $i| cut -f 3 -d '_')" "; \
    cut -f 1 $i | sort | uniq -c | awk '{val += $1; count +=1; \
    if ($1 == 1) sing += 1 } END{ printf("cov: %.2f\tsingletons: \
    %d\tuniq: %d\ttotal: %d\n", val/count,sing,count,val)
    }'; \
    done