I've just sent a file transfer with the pep.xml files and the command 
output. Thanks for taking a look into it.

Best,

Adam

On Thursday, August 30, 2018 at 1:03:24 PM UTC-5, David Shteynberg wrote:
>
> The errors above suggest that the pepXML files are not parser compliant 
> and cannot be read.  Sometimes this could be caused by bad characters in 
> the protein descriptions from the fasta database, you have to look at the 
> specific lines pointed to by the error messages to identify the exact 
> issue.  If you can post your failing files and I can take a look.
>
> Thanks,
> -David
>

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