If you can send me the inputs and options you're using for PeptideProphet I can see why it's failing and correct.
On Thu, Feb 21, 2019, 3:58 PM Michael Riffle <[email protected] wrote: > Thanks David, > > I'm certain PeptideProphet is finishing without error (I've tested in many > times.). It's just that it produces fewer XML attributes in the root > msms_pipeline_analysis node than InterProphet does. Because of these > missing attributes, PeptideProphet results are not being successfully > validated (by some software) and InterProphet results are. The exact syntax > is in my post, but adding xmlns=" > http://regis-web.systemsbiology.net/pepXML"; xmlns:xsi=" > http://www.w3.org/2001/XMLSchema-instance"; to the msms_pipeline_analysis > node in the PepXML output by PeptideProphet should solve the problem (it's > already there in the InterProphet output). > > Mike > > > On Thursday, February 21, 2019 at 3:47:43 PM UTC-8, David Shteynberg wrote: >> >> Hi Mike, >> >> It sounds like either PeptideProphet crashed and generated incomplete >> pepXML or another program upstream of PeptideProphet failed partly >> through. Can you check the standard and error outputs carefully for any >> clues? Let me know what you find. >> >> David >> >> On Thu, Feb 21, 2019, 12:22 PM Michael Riffle <[email protected] wrote: >> >>> Running TPP v5.2.0-b1 Flammagenitus Pre-release Beta, Build >>> 201809101205-7809 (Linux-x86_64)) >>> >>> Parsing pepXML files with Java using JAXB classes created from the >>> schema ( >>> http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v122.xsd). >>> >>> >>> I have noticed that PeptideProphet doesn't produce XML that can be >>> successfully parsed but that InterProphet does. Here is the error produced >>> from the PeptideProphet XML: >>> >>> [org.xml.sax.SAXParseException; systemId: >>> file:interact-2018_Oct_4_EhuxDDA_DA06.pep.xml; lineNumber: 3; columnNumber: >>> 253; The >>> >>> prefix "xsi" for attribute "xsi:schemaLocation" associated with an >>> element type "msms_pipeline_analysis" is not bound.] >>> >>> >>> The culprit is the <msms_pipeline_analysis> root element is missing >>> vital attributes when run by peptideprophet. >>> >>> PeptideProphet element: >>> <msms_pipeline_analysis xsi:schemaLocation=" >>> http://regis-web.systemsbiology.net/pepXML >>> /usr/local/tppschema/pepXML_v122.xsd" >>> summary_xml="/data/mass_spec/mriffle/brook.magnum.results/interact-2018_Oct_4_EhuxDDA_DA06.pep.xml"> >>> >>> InterProphet element: >>> <msms_pipeline_analysis xmlns=" >>> http://regis-web.systemsbiology.net/pepXML"; xmlns:xsi=" >>> http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation=" >>> http://regis-web.systemsbiology.net/pepXML >>> /tools/bin/TPP/tpp/schema/pepXML_v122.xsd" >>> summary_xml="/data/mass_spec/mriffle/brook.magnum.results/interact-2018_Oct_4_EhuxDDA_DA06.ipro.pep.xml"> >>> >>> If I add the following to the PeptideProphet msms_pipeline_analysis >>> element it works and parses happily: >>> xmlns="http://regis-web.systemsbiology.net/pepXML"; xmlns:xsi=" >>> http://www.w3.org/2001/XMLSchema-instance"; >>> >>> -- >>> 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]. 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.
