Hello, Where and how did you get the source database files? An ftp link off of ncbi?
I took a very quick look, and it seems that some of their larger files are distributed in portions that you then have to stitch together. If this is the case with your file, do you know how they were put together as one file? Perhaps this is where an errant character(s) is being introduced, corrupting the file. Can you take a small portion of the file (say, 100,000 lines) and look for "bad" characters? Anyone else had this issue out there? --Luis On Wed, Feb 1, 2012 at 2:55 PM, XC <[email protected]> wrote: > Hi there, > We 've been struggling with converting .dat file to pepXML file. > Finallly we nailed it down to bad NCBInr fasta files, since we always > got teh error message: Fail to get line from sequence database . So we > tried to search with a swissprot database. That worked. We tried > different version of NCBInr fasta files including 20120121, 20120128, > etc. But none of them works. I wonder, Anyone has the same probelm? > Know why? Anyway to fix it? Thanks a lot. > > xc > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
