Do you know how pepXMLViewer.cgi was built? It's meant to support large files...
On Wed, Mar 31, 2010 at 9:54 AM, dctrud <[email protected]> wrote: > Hi Brian, > > I thought about out of memory conditions, but am running on 64-bit > linux, and have 32GB of RAM, plus whilst running the cgi is using only > a very small fraction of that. > > Looked again and the file is *just* over the 2GB boundary, looks like > you're right, which has pointed me to the index file, which shows the > integer offset values have overflowed. > > Many Thanks, > > DT > > > On 31 Mar, 17:08, Brian Pratt <[email protected]> wrote: > > My guess would be that the parser is trying to fail gracefully on an out > of > > memory condition - it "forgets" part of the stream then is confused when > it > > hits an unmatched closing tag. > > > > But that's just a guess. Could also be about crossing the dread 2GB file > > size threshold. > > > > It's almost certainly about largeness, though. > > Brian > > > > On Wed, Mar 31, 2010 at 6:38 AM, dctrud <[email protected]> wrote: > > > All, > > > > > I'm having trouble with PepXMLViewer.cgi (4.3.1) on some very > > > large .pep.xml files. The cgi will exit with the error: > > > > > error with spreadsheet printing: XML parsing error: not well-formed > > > (invalid token), at xml file line 6298020, column 17 > > > > > This is for an export to Excel, but similar errors will also occur > > > when filtering the dataset in the web interface. > > > > > I've checked that the interact.pep.xml file is well formed with a > > > python script that uses expat to parse it (as per the cgi), and there > > > are no problems. Line 6298020 is the following end tag, which isn't an > > > invalid token: > > > > > </modification_info> > > > > > I've also checked that none of the protein descriptions in the file > > > contain < > " characters which could mess up the parsing earlier. Am > > > now out of ideas of what could be the cause, and wondering if anyone > > > has seen this problem, or has any ideas? > > > > > Many Thanks, > > > > > DT > > > > > -- > > > 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]<spctools-discuss%[email protected]> > <spctools-discuss%[email protected]<spctools-discuss%[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]<spctools-discuss%[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.
