Vidya, I noticed that you happen to have the string "<alpha>" in some of your sequence definition lines in your database. These are showing up in your interact.pep.xml and causing the parser to fail. Now we should be escaping anything that looks like xml in the sequence definition its possible we missed it somewhere. Could you try just removing the "<>" from the descriptions in the fasta file and rerunning? The four lines are:
>tr|Q9UMA4|Q9UMA4_HUMAN IFN-<alpha>2 protein (Fragment) OS=Homo sapiens GN=IFN-<alpha>2 PE=2 SV=1 >tr|A0N7E2|A0N7E2_HUMAN V<alpha>13 protein (Fragment) OS=Homo sapiens GN=V<alpha>13 PE=2 SV=1 >tr|A0N7E4|A0N7E4_HUMAN V<alpha>1 protein (Fragment) OS=Homo sapiens GN=V<alpha>1 PE=2 SV=1 -Joe On Fri, Nov 30, 2012 at 4:21 PM, Vidya Venkatraman <[email protected]>wrote: > 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]: > >> 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]>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<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<https://groups.google.com/d/msg/spctools-discuss/-/_OXYGwHUJmQJ> >>> . >>> To post to this group, send email to spctools...@googlegroups.**com. >>> To unsubscribe from this group, send email to spctools-discu...@** >>> googlegroups.com. >>> >>> For more options, visit this group at http://groups.google.com/** >>> group/spctools-discuss?hl=en<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. > -- 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.
