Hi, I have been installed TPP4.8.0 on Windows 7. Unfortunately I had no success yet for processing MS-GF+ files. The error I am seeing is the following:
*command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" MINPROB=0.05 PPM" exited with non-zero exit code: -1073741819* Not quite sure how I can get TPP to smoothly process the Ms-GF+ files. Any advice is greatly appreciated. HFaz On Friday, July 24, 2015 at 8:35:57 PM UTC-4, Jesse wrote: > > David, Joseph, > > Awesome everything works now with version 4.8.0 > > Thank you! > Jesse > > On Friday, July 24, 2015 at 2:33:05 PM UTC-7, David Shteynberg wrote: >> >> Hello Jesse, >> >> >> I think the issue is that ProteinProphet may not be finding the database >> used in the search. Can you run RefreshParser on the commandline as >> follows: >> >> RefreshParser >> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Kac.GluC.all.interact.pep.xml >> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Ecoli.fasta >> >> Then try to rerun ProteinProphet on the commandline >> >> ProteinProphet >> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Kac.GluC.all.interact.pep.xml >> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Kac.GluC.all.interact.prot.xml >> XML >> >> >> Let me know if you see any errors. >> >> Thank you, >> -David >> >> On Fri, Jul 24, 2015 at 2:19 PM, Joseph Slagel < >> [email protected]> wrote: >> >>> Jesse, >>> >>> Yes, I think David pinpointed an issue. It appears as if you >>> downloaded a developer alpha build of TPP. As an alpha build, its expected >>> to have lots of problems as it gets tested and they get fixed. I'd >>> recommend downloading the latest stable TPP release, 4.8.0, from >>> sourceforge, >>> http://sourceforge.net/projects/sashimi/files/latest/download?source=files >>> >>> -Joe >>> >>> >>> On Fri, Jul 24, 2015 at 2:11 PM, David Shteynberg < >>> [email protected]> wrote: >>> >>>> Hi Jesse, >>>> >>>> This issue seems unrelated to the issue that I just corrected in >>>> InteractParser. >>>> >>>> It appears that on your system everything is installed to C:\TPP\bin >>>> whereas it should install to C:\Inetpub\tpp-bin. Are you perhaps Which >>>> version are you installing? Can you try this command in the commandline >>>> to >>>> see if it gives you any additional messages? >>>> >>>> Thank you, >>>> >>>> -David >>>> >>>> On Fri, Jul 24, 2015 at 1:15 PM, Jesse <[email protected]> wrote: >>>> >>>>> Hi David, >>>>> >>>>> Now I'm almost certain there is a problem with the installation on my >>>>> new systems. TPP wont even convert RAW files or download spectral >>>>> libraries. Any suggestions about where to start? >>>>> >>>>> *EXECUTING: C:/TPP/bin/msconvert >>>>> c:/Inetpub/wwwroot/ISB/data/dbase/OR20080317_S_SILAC-LH_1-1_01.RAW -v >>>>> --mzXML -o c:/Inetpub/wwwroot/ISB/data/dbase --filter "peakPicking true >>>>> [1,2]" * >>>>> >>>>> *Command FAILED* >>>>> RETURN CODE:13568 >>>>> >>>>> Best, >>>>> Jesse >>>>> >>>>> On Thursday, July 23, 2015 at 2:01:02 PM UTC-7, Jesse wrote: >>>>>> >>>>>> Hi David, >>>>>> >>>>>> I just sent you a link to the files with my new email address. I >>>>>> tried without the pI model and I got the same error. I suspect a >>>>>> problem >>>>>> with the network settings on the computers at work. >>>>>> >>>>>> Thanks for looking into this for me. >>>>>> >>>>>> Best, >>>>>> Jesse >>>>>> ------------------------------ >>>>>> *From:* [email protected] [[email protected]] >>>>>> on behalf of David Shteynberg [[email protected]] >>>>>> >>>>>> *Sent:* Thursday, July 23, 2015 11:58 AM >>>>>> *To:* spctools-discuss >>>>>> *Subject:* Re: [spctools-discuss] Re: Processing MSGF+ searches >>>>>> >>>>>> Hello Jesse, >>>>>> >>>>>> >>>>>> I am not sure that I can pinpoint the error without access to your >>>>>> file. Is this possible? Otherwise you can try the analysis with the >>>>>> following PeptideProphetParser options removing PI model which has not >>>>>> been >>>>>> extensively tested through MSGF+ and could be the culprit. >>>>>> >>>>>> PeptideProphetParser >>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.0 >>>>>> CLEVEL=2.5 >>>>>> PPM DECOYPROBS ACCMASS NONTT NONPARAM DECOY=XXX_ IGNORECHG=1 >>>>>> >>>>>> If this works then the problem is with the pI model. >>>>>> >>>>>> Let me know if you can forward me your test.interact.pep.xml file to >>>>>> test with. >>>>>> >>>>>> Thank you, >>>>>> -David >>>>>> >>>>>> On Wed, Jul 22, 2015 at 7:57 PM, Jesse <[email protected]> wrote: >>>>>> >>>>>>> Hi David, >>>>>>> >>>>>>> I'm having problems recently running PeptideProphet on MSGF+ search >>>>>>> output of GluC digests. I tried the perl script you suggest but I'm >>>>>>> not >>>>>>> sure if it does anything because I'm not sure what it is supposed to >>>>>>> do. >>>>>>> That line is meant to replace a single "\" with "-", correct? It seems >>>>>>> to >>>>>>> start OK but then it quits. The GUI then prints return code: 65280. If >>>>>>> you could make a quick suggestion as to whether you think the problem >>>>>>> is my >>>>>>> pep.xml files again or my install I would greatly appreciate it. I >>>>>>> tried >>>>>>> both the development release and 4.8. >>>>>>> >>>>>>> C:/TPP/bin/xinteract (TPP v5.0.0a2 Development, Build xxxx-xxxx >>>>>>> (x86_64)) >>>>>>> PPM mode in Accurate Mass Model ... >>>>>>> PPM mode in Accurate Mass Model ... >>>>>>> >>>>>>> running: "C:/TPP/bin/InteractParser >>>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" >>>>>>> "150624_0002_CR1_GluC_Xyl_0p4_rep1b.pep.XML" >>>>>>> "150624_0003_CR1_GluC_Xyl_4_rep1.pep.XML" >>>>>>> "150624_0004_CR1_GluC_Glc_0p4_rep1.pep.XML" >>>>>>> "150624_0005_CR1_GluC_Glc_4_rep1.pep.XML" >>>>>>> "150624_0007_CR1_GluC_Xyl_0p4_rep2.pep.XML" >>>>>>> "150624_0008_CR1_GluC_Xyl_4_rep2.pep.XML" >>>>>>> "150624_0009_CR1_GluC_Glc_0p4_rep2.pep.XML" >>>>>>> "150624_0010_CR1_GluC_Glc_4_rep2.pep.XML" >>>>>>> "150624_0012_CR1_GluC_Xyl_0p4_rep3.pep.XML" >>>>>>> "150624_0014_CR1_GluC_Xyl_4_rep3.pep.XML" >>>>>>> "150624_0015_CR1_GluC_Glc_0p4_rep3.pep.XML" >>>>>>> "150624_0016_CR1_GluC_Glc_4_rep3.pep.XML" -L"7" -E"nonspecific"" >>>>>>> file 1: 150624_0002_CR1_GluC_Xyl_0p4_rep1b.pep.XMLWARNING: empty >>>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> file 2: 150624_0003_CR1_GluC_Xyl_4_rep1.pep.XMLWARNING: empty raw_data >>>>>>> in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> file 3: 150624_0004_CR1_GluC_Glc_0p4_rep1.pep.XMLWARNING: empty >>>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> file 4: 150624_0005_CR1_GluC_Glc_4_rep1.pep.XMLWARNING: empty raw_data >>>>>>> in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> file 5: 150624_0007_CR1_GluC_Xyl_0p4_rep2.pep.XMLWARNING: empty >>>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> file 6: 150624_0008_CR1_GluC_Xyl_4_rep2.pep.XMLWARNING: empty raw_data >>>>>>> in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> file 7: 150624_0009_CR1_GluC_Glc_0p4_rep2.pep.XMLWARNING: empty >>>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> file 8: 150624_0010_CR1_GluC_Glc_4_rep2.pep.XMLWARNING: empty raw_data >>>>>>> in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> file 9: 150624_0012_CR1_GluC_Xyl_0p4_rep3.pep.XMLWARNING: empty >>>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> file 10: 150624_0014_CR1_GluC_Xyl_4_rep3.pep.XMLWARNING: empty >>>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> file 11: 150624_0015_CR1_GluC_Glc_0p4_rep3.pep.XMLWARNING: empty >>>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> file 12: 150624_0016_CR1_GluC_Glc_4_rep3.pep.XMLWARNING: empty >>>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>>> Failed to open input file >>>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzML'.WARNING: >>>>>>> cannot open data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzML >>>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> SUCCESS: CORRECTED data file >>>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzXML >>>>>>> in msms_run_summary tag ... >>>>>>> processed altogether 186504 results >>>>>>> INFO: Results written to file: >>>>>>> C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml >>>>>>> command completed in 86 sec >>>>>>> >>>>>>> running: "C:/TPP/bin/DatabaseParser >>>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml"" >>>>>>> command completed in 2 sec >>>>>>> >>>>>>> running: "C:/TPP/bin/RefreshParser >>>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" >>>>>>> "C:\Jesse\Ecoli.fasta"" >>>>>>> - Searching the tree...opening "c:/Jesse/Ecoli.fasta" as >>>>>>> "c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Ecoli.fasta" >>>>>>> >>>>>>> - Linking duplicate entries... - Printing results... >>>>>>> >>>>>>> - Building Commentz-Walter keyword tree...command completed in 22 sec >>>>>>> >>>>>>> running: "C:/TPP/bin/PeptideProphetParser >>>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.05 >>>>>>> CLEVEL=2.5 PPM PPM ACCMASS PI NONTT NONPARAM DECOY=XXX_ IGNORECHG=1" >>>>>>> using Accurate Mass Bins >>>>>>> using PPM mass difference >>>>>>> using pI >>>>>>> Using Decoy Label "XXX_". >>>>>>> Ignoring charge 1+ spectra. >>>>>>> Not using ntt model >>>>>>> Using non-parametric distributions >>>>>>> (MS-GF+)WARNING: Support of MSGF+ may not be full. There exist known >>>>>>> issues with the way MSGF+ encodes certain modifications in pep.xml that >>>>>>> may not be correct. Also, high-scoring DECOY have been observed in >>>>>>> MSGF+ analysis. The user is encouraged to be vigilant in comparing >>>>>>> model estimated error-rates to the DECOY-estimated error-rates to make >>>>>>> sure the two agree and set CLEVEL parameter accordingly: see >>>>>>> http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#What_is_CLEVEL_and_when_do_I_use_it.3F >>>>>>> adding Accurate Mass mixture distr >>>>>>> adding pI mixture distr >>>>>>> init with MS-GF+ nonspecific >>>>>>> >>>>>>> command "C:/TPP/bin/PeptideProphetParser >>>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.05 >>>>>>> CLEVEL=2.5 PPM PPM ACCMASS PI NONTT NONPARAM DECOY=XXX_ IGNORECHG=1" >>>>>>> failed: Unknown error >>>>>>> >>>>>>> command "C:/TPP/bin/PeptideProphetParser >>>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.05 >>>>>>> CLEVEL=2.5 PPM PPM ACCMASS PI NONTT NONPARAM DECOY=XXX_ IGNORECHG=1" >>>>>>> exited with non-zero exit code: 255 >>>>>>> QUIT - the job is incomplete >>>>>>> >>>>>>> >>>>>>> On Thursday, July 9, 2015 at 2:33:16 PM UTC-7, [email protected] >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi David, >>>>>>>> >>>>>>>> I can cope with the command line. Thanks for the info I never would >>>>>>>> have worked that one out... >>>>>>>> >>>>>>>> Peter >>>>>>>> >>>>>>>> On Thursday, July 9, 2015 at 2:55:41 PM UTC+10, [email protected] >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> >>>>>>>>> I want to use the TPP to combine, Mascot, X!Tandem and MSGF+ >>>>>>>>> searches (amongst other things). I'm having trouble getting around >>>>>>>>> some of >>>>>>>>> the basics. I have successfully used the TPP in the past to process >>>>>>>>> samples, but only with Mascot data. >>>>>>>>> >>>>>>>>> Once I get my MSGF+ output files converted to pepXML I should be >>>>>>>>> fine. I cannot work out how I get the MSGF+ files converted. The >>>>>>>>> output >>>>>>>>> generated by MSGF+ is an mzid file. I am also unclear as to where the >>>>>>>>> database (with decoys) and mzXML files, used for searching, need to >>>>>>>>> be >>>>>>>>> located when generating this pepXML file. I have noticed error >>>>>>>>> messages in >>>>>>>>> the logs about accessing the database and mzXML file. I am generally >>>>>>>>> using >>>>>>>>> the Petunia interface as it's much nicer to work with multiple files. >>>>>>>>> >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> >>>>>>>>> Peter >>>>>>>>> >>>>>>>> -- >>>>>>> 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 http://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 http://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 http://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 http://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> >>> >>> -- >>> Joe Slagel >>> Institute for Systems Biology >>> [email protected] >>> >>> -- >>> 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 http://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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
