Hi Ankit, For me it works as follows:
1. Convert with idconvert: idconvert file.mzid --pepXML 2. Then change the extension of the files from *.pepXML to *.pep.xml then you will se them in Petunia. 3. The use Update Paths in Petunia to update the paths of the Raw files and database. (That's one of the errors as it cannot find were the RAW files are located. Sometimes the pepxml generated has a different path structure and this leads to errors when running the TPP tools. Best, Alejandro On Tuesday, January 15, 2019 at 7:17:12 PM UTC+1, Ankit Balhara wrote: > > Hi all, > > I was analyzing my data using MS-GF+ and then converted its output .mzid > to .pepXML using idconvert. Then I tried to analyze them using > Peptideprophet of the TPP GUI 'Petunia'. I choose the Pipeline- Tandem. > Then it is not showing the files, so I converted the .pepXML files to .XML > format by using "save as" option in notepad. I have three files. After that > I ran those files again on Peptideprophet of the TPP GUI 'Petunia'. But > following error message is appearing. I also used the non-parametric model > during analysis. > > C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 > (Windows_NT-x86_64)) > PPM mode in Accurate Mass Model ... > running: "C:/TPP/bin/InteractParser > "/tmp/a02972/params/MS-GF/interact.pep.xml" "PQC1_Q1.XML" "PQC1_Q2.XML" > "PQC1_Q3.XML" -L"7"" file 1: PQC1_Q1.XMLWARNING: empty raw_data in > msms_run_summary tag... trying .mzML ...WARNING: cannot open data file > c:/TPP/data/params/MS-GF/PQC1_Q1.mzML in msms_run_summary tag... trying > .mzXML ...WARNING: CANNOT correct data file > c:/TPP/data/params/MS-GF/PQC1_Q1.mzXML in msms_run_summary tag...WARNING: > empty raw_data in msms_run_summary tag... trying .mzML ...WARNING: cannot > open data file c:/TPP/data/params/MS-GF/PQC1_Q1.mzML in msms_run_summary > tag... trying .mzXML ...WARNING: CANNOT correct data file > c:/TPP/data/params/MS-GF/PQC1_Q1.mzXML in msms_run_summary tag... > file 2: PQC1_Q2.XMLWARNING: empty raw_data in msms_run_summary tag... trying > .mzML ...WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q2.mzML > in msms_run_summary tag... trying .mzXML ...WARNING: CANNOT correct data file > c:/TPP/data/params/MS-GF/PQC1_Q2.mzXML in msms_run_summary tag...WARNING: > empty raw_data in msms_run_summary tag... trying .mzML ...WARNING: cannot > open data file c:/TPP/data/params/MS-GF/PQC1_Q2.mzML in msms_run_summary > tag... trying .mzXML ...WARNING: CANNOT correct data file > c:/TPP/data/params/MS-GF/PQC1_Q2.mzXML in msms_run_summary tag... > file 3: PQC1_Q3.XMLWARNING: empty raw_data in msms_run_summary tag... trying > .mzML ...WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q3.mzML > in msms_run_summary tag... trying .mzXML ...WARNING: CANNOT correct data file > c:/TPP/data/params/MS-GF/PQC1_Q3.mzXML in msms_run_summary tag...WARNING: > empty raw_data in msms_run_summary tag... trying .mzML ...WARNING: cannot > open data file c:/TPP/data/params/MS-GF/PQC1_Q3.mzML in msms_run_summary > tag... trying .mzXML ...WARNING: CANNOT correct data file > c:/TPP/data/params/MS-GF/PQC1_Q3.mzXML in msms_run_summary tag... > processed altogether 13489 results > INFO: Results written to file: /tmp/a02972/params/MS-GF/interact.pep.xml > command completed in 6 sec > running: "C:/TPP/bin/DatabaseParser > "/tmp/a02972/params/MS-GF/interact.pep.xml""command completed in 0 sec > running: "C:/TPP/bin/RefreshParser > "/tmp/a02972/params/MS-GF/interact.pep.xml" "C:\MS-GF\Human.fasta"" > - Searching the tree... > - Linking duplicate entries... > - Printing results... > > - Building Commentz-Walter keyword tree...command completed in 4 sec > running: "C:/TPP/bin/PeptideProphetParser > "/tmp/a02972/params/MS-GF/interact.pep.xml" MINPROB=0.05 PPM NONPARAM"using > PPM mass differenceWARNING: Cannot non-parametric distributions without > decoys! > (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.3FWARNING: > MSGFPL only support semi-parametric PeptideProphet modelling, which relies > on a DECOY search.WARNING: MSGFPL only support semi-parametric PeptideProphet > modelling, which relies on a DECOY search.WARNING: MSGFPL only support > semi-parametric PeptideProphet modelling, which relies on a DECOY > search.WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, > which relies on a DECOY search.WARNING: MSGFPL only support semi-parametric > PeptideProphet modelling, which relies on a DECOY search.WARNING: MSGFPL only > support semi-parametric PeptideProphet modelling, which relies on a DECOY > search.WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, > which relies on a DECOY search. > init with MS-GF+ trypsin > MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: > UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN > > INFO: Processing standard MixtureModel ... > PeptideProphet (TPP v5.1.0 Syzygy, Build 201711031215-7670 > (Windows_NT-x86_64)) AKeller@ISB > read in 0 1+, 6282 2+, 5137 3+, 1488 4+, 0 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > Iterations: .........10.........20 > > command "C:/TPP/bin/PeptideProphetParser > "/tmp/a02972/params/MS-GF/interact.pep.xml" MINPROB=0.05 PPM NONPARAM" > failed: Unknown error > > command "C:/TPP/bin/PeptideProphetParser > "/tmp/a02972/params/MS-GF/interact.pep.xml" MINPROB=0.05 PPM NONPARAM" exited > with non-zero exit code: -1073741819 > QUIT - the job is incomplete > > Could anybody please help me out to fix this problem. > > > Thanks. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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