Hi Tiannan, The purpose of the PepXMLViewer step within xinteract is to pre-generate an index of peptide entries that the actual viewer can use later on. This is (usually) quite convenient, as generating this index can sometimes take a while; doing it in advance translates into the user being able to very quickly opening the output file in the viewer. This step can be skipped with no loss of data or impact to the analysis.
It is quite strange that the index step is mis-behaving like that; it would be interesting to see what is being written to this file. Can you send us what the first 100 lines and the last 100 lines in that .index file are? Cheers, --Luis On Mon, Jan 24, 2011 at 10:34 PM, tiannan <[email protected]> wrote: > hi, > > I can also successfully analyze the files in d drive, if I skip the > command "PepXMLViewer.cgi". Now the question is what's > PepXMLViewer.cgi for when we execute the commands in DOS.Thanks! > > cheers, > Tiannan > > > On Jan 25, 12:04 pm, Vishal Swaroop <[email protected]> wrote: > > Hi, > > > > We have successfully implemented storing files under D: drive some time > > back... > > > > Not sure, but do you "tmp" folder under c: root.... > > > > Is it possible to send your apache config file? > > > > Thanks > > > > On Mon, Jan 24, 2011 at 8:29 AM, tiannan <[email protected]> wrote: > > > hi, > > > > > I'm trying to use TPP v4.4 to analyze my multiple Mascot dat > > > search result files. It works in analyzing few dat files in my hands, > > > but when I tried to analyze ~30 files, the PepXMLViewer.cig is > > > generating a huge file named as interact.pep.xml.index (>3G now, and > > > still growing..). My question is: is it normal to have such a huge > > > file, or is it a bug? It may be worth noting that my dat files are not > > > stored in c:/Inetpub/wwwroot/ISB/data/, but in a D drive. > > > > > My protocols are as below (executed in DOS): > > > > > 1, convert dat to pepXML using Mascot2XML. > > > > > 2, convert multiple (~30) pepXML to interact.pep.xml using xinteract. > > > It shows: > > > > > >running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > > > MINPROB=0.05" > > > ... > > > >running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml" > > > ... > > > >running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" > > > ... > > > >running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" > > > "c:/Inetpub/wwwroot/ISB/db/myDatabase.fasta"" > > > ... > > > >>running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > > > d:/myMSdata/interact.pep.xml" > > > > > 3, I noticed there was a file named as interact.pep.xml had been > > > generated rapidly, but the last command in step 2 is still generating > > > huge interact.pep.xml.index which slowly grows to >3G, and it is still > > > growing. > > > > > A warning showed several time is as below: > > > > > problem (ph8): d:/myMSdata/interact.pep.xml is not mounted under > > > webserver root: c:/Inetpub/wwwroot/ > > > > > Thanks a lot! > > > > > Best regards, > > > Tiannan > > > > > -- > > > 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.
