Shredded Fastaq sequences generate weird srst2 output for most and antibioitc resistance genotyping

Hi there, I tried shredding my fasta sequences to fastq using fastaq module they were converted successfully to paired end sequences however, were not handled correctly by srst2. The output it generated comprised of tons of hits for those seven MLST housekeeping alleles and I see similar unexpected results for antibioitc resistance genes. Any suggestions why it might happen?
