Hello David! I have the same problem. After running the command I've got this info message:
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\a04048\': File exists command "C:\TPP\bin\mkdir.exe -p "/tmp/a04048/"" failed: Operation not permitted could not create temp dir /tmp/a04048/, working in data directory running: "C:/TPP/bin/InteractParser "interact.pep.xml" "search.pep.xml" -L"7"" And after this there is new file interact.pep.xml.tmp.a04100 created in directory C:\tmp\a05484 while my data directory is C:\TPP\data понедельник, 20 ноября 2017 г., 8:38:59 UTC+3 пользователь David Shteynberg написал: > > 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 <[email protected] > <javascript:>> 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 <[email protected]> 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 <[email protected]> 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 [email protected]. >>>>>> To post to this group, send email to [email protected]. >>>>>> 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 [email protected]. >>>> To post to this group, send email to [email protected]. >>>> 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 [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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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