Hello again Malcolm, There are several of these non-ascii characters in the protXML file that you sent. After I removed them I was able to open the file in ProtXMLViewer. Also the syntax errors from tpp2mzid went away (although I wasn't able to convert your file without the associated pepXML data.) Please let us know if you are able to resolve this issue on your end.
Cheers, -David On Fri, Jun 10, 2022 at 7:35 AM Malcolm Cook <[email protected]> wrote: > I just got TPP installed and am trying to [test the installation with a > sample dataset]( > http://tools.proteomecenter.org/wiki/index.php?title=TPP_6.1.0:_Installing_on_Ubuntu_20.04_LTS#Testing_the_installation_with_a_sample_dataset_.28optional.29 > ) > > I am getting an error with tpp2mzid parsing ProteinProphet output (here > is the full file > <https://ftp.stowers.org/public/mec/tpp/interact.prot.xml>). > > Reviewing the ISB/SPC Trans Proteomic Pipeline :: Jobs logs I read our > ProteinProphet completed with success: > > > *Finished. Results written to: > /data/tpp/tests/QuickYeastUPS1/interact.prot.xmlhowever * > however trying to process it with tpp2mzid gives error > > > > > *Reading: > /data/tpp/tests/QuickYeastUPS1/interact.prot.xml/data/tpp/tests/QuickYeastUPS1/interact.prot.xml(148) > : error 4: Syntax error parsing XML.Failed to read protXML: > /data/tpp/tests/QuickYeastUPS1/interact.prot.xmlmanually * > inspecting this file it looks like a well formed big ball of XML to my > eyes: > > > > > > > > > > > > > > > *<?xml version="1.0" encoding="UTF-8"?><?xml-stylesheet type="text/xsl" > href="http://hd1991356yb/tests/QuickYeastUPS1/interact.prot.xsl > <http://hd1991356yb/tests/QuickYeastUPS1/interact.prot.xsl>"?><protein_summary > xmlns="http://regis-web.systemsbiology.net/protXML > <http://regis-web.systemsbiology.net/protXML>" > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance > <http://www.w3.org/2001/XMLSchema-instance>" > xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v9.xsd > <http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v9.xsd>" > summary_xml="/data/tpp/tests/QuickYeastUPS1/interact.prot.xml"><protein_summary_header > reference_database="/data/tpp/tests/QuickYeastUPS1/Yeast_UPS_cRAP.fasta" > residue_substitution_list="I -> L" > source_files="/data/tpp/tests/QuickYeastUPS1/interact.ipro.pep.xml" > source_files_alt="/data/tpp/tests/QuickYeastUPS1/interact.ipro.pep.xml" > min_peptide_probability="0.20" min_peptide_weight="0.50" > num_predicted_correct_prots="98.6" num_input_1_spectra="0" > num_input_2_spectra="348" num_input_3_spectra="70" num_input_4_spectra="0" > num_input_5_spectra="0" initial_min_peptide_prob="0.05" > total_no_spectrum_ids="357.6" sample_enzyme="trypsin"><program_details > analysis="proteinprophet" time="2022-06-09T09:15:57" version=" > Insilicos_LabKey_C++ (TPP v6.1.0 Parhelion, Build 202206081159-exported > (Linux-x86_64))"><proteinprophet_details occam_flag="Y" groups_flag="Y" > degen_flag="Y" nsp_flag="Y" fpkm_flag="N" initial_peptide_wt_iters="2" > nsp_distribution_iters="3" final_peptide_wt_iters="0" > run_options="IPROPHET"> <nsp_information > neighboring_bin_smoothing="Y"><yadda_yadda_yadda>...</yadda_yadda_yadda></protein_group></protein_summary>* > trying to run tpp2mzid from the command line sheds little light: > > > > > > > > > */usr/local/tpp/bin/tpp2mzid > /data/tpp/tests/QuickYeastUPS1/interact.prot.xmltpp2mzid v0.9.11 (May 19 > 2022), copyright Mike Hoopmann, Institute for Systems Biology.Built using > mzIMLTools: 1.2.6 Mar 21 2022Built using NeoPepXMLParser: 1.0.2 2022 > MAY 17Built using NeoProtXMLParser: 1.0.0 2022 MAY 19Reading: > /data/tpp/tests/QuickYeastUPS1/interact.prot.xml/data/tpp/tests/QuickYeastUPS1/interact.prot.xml(148) > : error 4: Syntax error parsing XML.Failed to read protXML: > /data/tpp/tests/QuickYeastUPS1/interact.prot.xml* > how to diagnose/debug/fix? > > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/e09ec315-2321-4e11-b97d-dbba51fb1d3an%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/e09ec315-2321-4e11-b97d-dbba51fb1d3an%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-kYi1%2B3CkQeZbD7c_UBSk%2BtW2hXT13AkzTrLttO3ecLw%40mail.gmail.com.
