Assigning STs to files that failed QC

Hi I have about 3 samples that I have tried on multiple occasions to upload to the server however they keep failing QC. The sequencing on them has been rerun but still is not working. I believe they are new sequence types. Is there a way to find out why they are failing QC or whether I can manually upload the 7 loci for MLST and get a ST assigned to these isolates?

Thanks .