I am unable to reproduce this error when I download and run the tutorial on
my windows or linux (ubuntu) machines with this tutorial data. Perhaps you
can confirm that the fasta file you have is not getting corrupted somehow
during your download or processing. Thanks.
-David
On Fri, Jun 10, 2022 at 1:37 PM Malcolm Cook <malcolm.c...@gmail.com> wrote:
> I discovered the issue. I believe you have a bug.
>
> In my hands, when the fasta deflines in Yeast_UPS_cRAP.fasta are longer
> than 120 characters they get truncated and a non-breaking space appended.
>
> Running the demo pipeline runs to completion if I first fix this problem
> with:
>
>
> *sudo -u apache bash -c 'perl -pi -e "s|^(>.{119,119})(.*)\$|\$1|"
> /data/tpp/tests/QuickYeastUPS1/Yeast_UPS_cRAP.fasta'*
>
>
> On Friday, June 10, 2022 at 1:14:08 PM UTC-5 Malcolm Cook wrote:
>
>> Thank you. I concur deleting those characters resolves the issue.
>>
>> My colleague Gabriel actually was running the tutorial test. I will ask
>> him to chime in if he did anything other than follow the steps given.
>>
>> On Friday, June 10, 2022 at 12:03:08 PM UTC-5 David Shteynberg wrote:
>>
>>> 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 <malcol...@gmail.com>
>>> 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!
>>>>
>>>> --
>>>>
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>>>>
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