I think I solved this problem. The issue is with the decoys and how they are named in MS-GF+. Their names don't start with REV but with XXX.
On Wednesday, September 23, 2015 at 4:33:41 PM UTC-4, HFaz wrote: > > 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.
