Hi Alejandro, Thanks a lot for your help, I tried this approach, and it is working.
Regards Ankit [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> 06/02/19, 2:26:55 PM On Sun, 2 Jun 2019 at 05:05, Alejandro <[email protected]> wrote: > 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. > 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. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/2693dbb4-9b62-43e6-b75f-ed4f0222271b%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/2693dbb4-9b62-43e6-b75f-ed4f0222271b%40googlegroups.com?utm_medium=email&utm_source=footer> > . > 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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