Hello Elkan, Although unlikely, the dashes in your filename could be the issue. In my email on this thread I mentioned that only alphanumerics and underscores "_" should be utilized. If that fails there is a problem with the pep.xml file itself, that you would need to troubleshoot. How was the file generated?
-David On Fri, Nov 17, 2017 at 12:46 AM, Elkan Dong <np.dong...@gmail.com> wrote: > I'm using the newest version of TPP, but encountered the same error when > using PeptideProphet. The file name I used looks like > I08-F4-SAX1.pep.xml > Any solution? > > Thanks. > > Elkan > > > 在 2017年6月20日星期二 UTC+8上午1:28:34，David Shteynberg写道： >> >> Hello Ada, >> >> One immediate problem I notice is that your files contain parenthesis >> character. Please name your files using only alphanumeric and underscore >> character, please no special characters or whitespace. Also, you might >> consider using comet search engine, support for which is more streamlined >> in the TPP. >> >> Cheers, >> -David >> >> On Mon, Jun 19, 2017 at 9:46 AM, Ada A <ada.an...@gmail.com> wrote: >> >>> Hello, >>> >>> I was trying to run peptide analysis with PeptideProphet but it keeps >>> showig me error... >>> I was using dimethyl labeling technique and peptides were identified >>> using Mascot. I exported all data from Mascot, uploaded here and it fails >>> to do anything. I was wondering whether anyone could advice me what should >>> I do with it? I would be grateful for some help. >>> >>> Here is what it shows me: >>> >>> C:/TPP/bin/xinteract (TPP v5.0.0 Typhoon, Build 201610111222-7423 >>> (Windows_NT-x86_64)) >>> PPM mode in Accurate Mass Model ... >>> C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a09964\': File exists >>> >>> command "C:\TPP\bin\mkdir.exe -p "/tmp/a09964/"" failed: Operation not >>> permitted >>> could not create temp dir /tmp/a09964/, working in data directory >>> running: "C:/TPP/bin/InteractParser "interact.pep.xml" "H7(3).pep.xml" >>> "h7(3).xml" -L"7"" file 1: H7(3).pep.xmlWARNING: empty raw_data in >>> msms_run_summary tag ... trying mzML ... >>> Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data >>> file c:/TPP/data/.mzML in msms_run_summary tag ...... trying .mzXML ... >>> Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT data >>> file c:/TPP/data/.mzXML in msms_run_summary tag ...WARNING: empty raw_data >>> in msms_run_summary tag ... trying mzML ... >>> Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data >>> file c:/TPP/data/.mzML in msms_run_summary tag ...... trying .mzXML ... >>> Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT data >>> file c:/TPP/data/.mzXML in msms_run_summary tag ... >>> >>> >>> >>> Kind Regards, >>> >>> Ada >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to spctools-discu...@googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.com. >>> Visit this group at https://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
