Looks like this is not an error message but some information. It seems that the process actually got past this point. Are you certain that the command dies here? Can you see the output file interact.pep.xml in your working directory? You can try deleting the directory C: /tmp/a04316/ to seeing this particular message.
-David On Sun, Nov 19, 2017 at 6:17 PM, Elkan Dong <np.dong...@gmail.com> wrote: > Hi David, > > Still encountered the problem. > > C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 > (Windows_NT-x86_64)) > PPM mode in Accurate Mass Model ... > C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a04316\': File exists > > command "C:\TPP\bin\mkdir.exe -p "/tmp/a04316/"" failed: Operation not > permitted > could not create temp dir /tmp/a04316/, working in data directory > > running: "C:/TPP/bin/InteractParser "interact.pep.xml" > "I17F1SAX.decoy.pep.xml" "I17F1SAX.pep.xml" "I17F1SCX.decoy.pep.xml" > "I17F1SCX.pep.xml" "I17F2SAX.decoy.pep.xml" "I17F2SAX.pep.xml" > "I17F2SCX.decoy.pep.xml" "I17F2SCX.pep.xml" "I17F3SAX.decoy.pep.xml" > "I17F3SAX.pep.xml" "I17F3SCX.decoy.pep.xml" "I17F3SCX.pep.xml" > "I17F4SAX.decoy.pep.xml" "I17F4SAX.pep.xml" "I17F4SCX.decoy.pep.xml" > "I17F4SCX.pep.xml" "I17F5SAX.decoy.pep.xml" "I17F5SAX.pep.xml" > "I17F5SCX.decoy.pep.xml" "I17F5SCX.pep.xml" "I17F6SAX.decoy.pep.xml" > "I17F6SAX.pep.xml" "I17F6SCX.decoy.pep.xml" "I17F6SCX.pep.xml" > "I17F7SAX.decoy.pep.xml" "I17F7SAX.pep.xml" "I17F7SCX.decoy.pep.xml" > "I17F7SCX.pep.xml" "I17F8SAX.decoy.pep.xml" "I17F8SAX.pep.xml" > "I17F8SCX.decoy.pep.xml" "I17F8SCX.pep.xml" -L"5"" > > > Regards, > > Elkan > > > 在 2017年11月17日星期五 UTC+8下午10:47:29，David Shteynberg写道： >> >> 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.do...@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-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. 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