Hi Joe, Thanks for your quick response. I have put all the remaining output files into dropbox now. Please take a look and let me know if you need any other information.
Vidya On Friday, November 30, 2012 6:44:45 PM UTC-5, [email protected] wrote: > > Hi Vidya, > > Thanks for providing such great detail on the issue and I'm sorry it isn't > working for you. We're taking a look at what you posted and there is an > error indicating invalid XML formatting in one of your files. > Unfortunately this is one of the ones that you haven't posted to dropbox. > Any chance you can upload the following file from your system (from the > "not working" case)? > > C:/Inetpub/wwwroot/ISB/data/data/interact.pep.xml" > > Thanks, > Joe > > On Fri, Nov 30, 2012 at 3:04 PM, Vidya Venkatraman > <[email protected]<javascript:> > > wrote: > >> Hi, >> >> I have encountered an issue wherein if I try to convert a mascot .dat >> file to pepxml, it does the conversion and when I try to use this pepxml >> to run peptideprophet and proteinprophet, it fails. >> >> I tried to check if .dat to pepxml conversion worked properly, but >> realised that when I click on the pepxml, nothing loads on the pepxml >> viewer and I also saw that usually there is an index file that is created >> and in this case, it did not create the index file as well. Just to make >> sure the .dat file is good, i was also able to open it up on Scaffold and >> see some proteins. >> >> This is the link to the shared dropbox folder called "TPP" >> https://www.dropbox.com/sh/4unsley0gir7jve/7D3-XANnj8 >> >> I have 2 folders there, one called "working files" where I tested a .dat >> file (from same samle, different fraction) conversion to pepxml and ran >> peptide and protein prophet and it worked successfully. The other folder >> called "not working files" has the .dat file which failed to run peptide >> and protein prophet. Also attached are .mzxml, .pepxml, the log of >> conversion from .dat to .pepxml and errorlog of conversion from pepxml to >> peptide and protein prophet along with screenshots. I have also included >> the fasta file I used in the "Fasta" folder. >> >> Can you anyone guide me as to what could have gone wrong? >> >> Thanks in advance, >> Vidya >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To view this discussion on the web visit >> https://groups.google.com/d/msg/spctools-discuss/-/_OXYGwHUJmQJ. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> To unsubscribe from this group, send email to >> [email protected] <javascript:>. >> 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 view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/sR6TGOvkegwJ. 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.
