Crux-Toolkit / Issues / #400 tide-search fails to parse MGF file (in search-for-xlinks branch)

William S Noble - 2016-06-22

Important update: for pwiz, the problem only shows up if I compile in Debug mode. If I use Release mode and the pwiz parser, the search completes successfully.

bash-4.1$ rm -fr crux-output ; /net/noble/vol1/home/noble/proj/crux/branches/crux-sfx-topn/Release/src/crux tide-search small.mgf ~peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
INFO: Creating index from '/net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta'
INFO: Running tide-index...
INFO: Writing results to output directory 'crux-output/tide-search.tempindex'.
INFO: Reading /net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta and computing unmodified peptides...
INFO: Writing decoy fasta...
INFO: Reading proteins
INFO: Precomputing theoretical spectra...
INFO: Beginning tide-search.
WARNING: The output directory 'crux-output' already exists.
Existing files will not be overwritten.
INFO: CPU: pyrrolysine.gs.washington.edu
INFO: Wed Jun 22 12:15:18 PDT 2016
INFO: Running tide-search...
INFO: Reading index crux-output/tide-search.tempindex
INFO: Converting small.mgf to spectrumrecords format
INFO: Parser could not determine scan numbers for this file, using ordinal numbers as scan numbers.
INFO: Reading spectra file crux-output/small.mgf.spectrumrecords.tmp
INFO: Sorting spectra
INFO: Running search
INFO: Time per spectrum-charge combination: 0.001960 s.
INFO: Average number of candidates per spectrum-charge combination: 0.965116
INFO: Elapsed time: 0.414 s
INFO: Finished crux tide-search.
INFO: Return Code:0
bash-4.1$

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Kaipo - 2016-06-22

It looks like another boost::lexical_cast issue, ProteoWizard tries to convert the charge but doesn't do any handling of the '+' as far as I can tell. I'll fix this issue in ProteoWizard and check if it resolves the issue.

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Kaipo - 2016-06-24

Actually, I made a fix for this and went to test it but I tried running it without the fix and I didn't get any error with either mstoolkit or proteowizard.

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- William S Noble - 2016-06-24
  
  Crud, you are right -- I just verified this. Apparently, the behavior only
  appears in the crux-sfx-topn branch. Sean, what is the feasibility of
  merging from the trunk into your branch, now that the mods handling is all
  fixed?
  
  Bill
  
  On Fri, Jun 24, 2016 at 11:02 AM, Kaipo kaipot@users.sf.net wrote:
  
  Actually, I made a fix for this and went to test it but I tried running it
  without the fix and I didn't get any error with either mstoolkit or
  proteowizard.
  
  [issues:#400] https://sourceforge.net/p/cruxtoolkit/issues/400/
  tide-search fails to parse MGF file*
  
  Status: open
  Milestone: post v2.0
  Labels: High priority
  Created: Wed Jun 22, 2016 07:13 PM UTC by William S Noble
  Last Updated: Wed Jun 22, 2016 08:52 PM UTC
  Owner: Kaipo
  Attachments:
  
  small.mgf
  https://sourceforge.net/p/cruxtoolkit/issues/400/attachment/small.mgf
  (274.9 kB; application/octet-stream)
  
  The tide-search command fails to parse the attached MGF file, irrespective
  of whether I use the pwiz or mstoolkit parser. In one case, it complains
  that it can't identify the format; in the other it complains about the line
  specifying the charge state.
  
  Here is a description of MGF:
  
  http://www.matrixscience.com/help/data_file_help.html
  
  I can't see any problem with the file I'm using.
  
  bash-4.1$ rm -fr crux-output;
  /net/noble/vol1/home/noble/proj/crux/branches/crux-sfx-topn/Debug/src/crux
  tide-search small.mgf
  ~peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
  INFO: Creating index from
  '/net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta'
  INFO: Running tide-index...
  INFO: Writing results to output directory
  'crux-output/tide-search.tempindex'.
  INFO: Reading
  /net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
  and computing unmodified peptides...
  INFO: Writing decoy fasta...
  INFO: Reading proteins
  INFO: Precomputing theoretical spectra...
  INFO: Beginning tide-search.
  WARNING: The output directory 'crux-output' already exists.
  Existing files will not be overwritten.
  INFO: CPU: pyrrolysine.gs.washington.edu
  INFO: Wed Jun 22 12:09:42 PDT 2016
  INFO: Running tide-search...
  INFO: Reading index crux-output/tide-search.tempindex
  INFO: Converting small.mgf to spectrumrecords format
  ERROR: [SpectrumList_MGF::parseSpectrum] Error parsing line at offset
  122: CHARGE=3+
  
  FATAL: Error converting small.mgf to spectrumrecords format
  bash-4.1$ rm -fr crux-output ;
  /net/noble/vol1/home/noble/proj/crux/branches/crux-sfx-topn/Debug/src/crux
  tide-search --spectrum-parser mstoolkit small.mgf
  ~peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
  INFO: Creating index from
  '/net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta'
  INFO: Running tide-index...
  INFO: Writing results to output directory
  'crux-output/tide-search.tempindex'.
  INFO: Reading
  /net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
  and computing unmodified peptides...
  INFO: Writing decoy fasta...
  INFO: Reading proteins
  INFO: Precomputing theoretical spectra...
  INFO: Beginning tide-search.
  WARNING: The output directory 'crux-output' already exists.
  Existing files will not be overwritten.
  INFO: CPU: pyrrolysine.gs.washington.edu
  INFO: Wed Jun 22 12:10:10 PDT 2016
  INFO: Running tide-search...
  INFO: Reading index crux-output/tide-search.tempindex
  INFO: Converting small.mgf to spectrumrecords format
  Unknown file format
  FATAL: MSToolkit: Error reading spectra file:
  /net/noble/vol4/noble/user/noble/proj/crux-projects/2016gaussian/results/bill/2016-06-22segfault/small.mgf
  
  Sent from sourceforge.net because you indicated interest in
  https://sourceforge.net/p/cruxtoolkit/issues/400/
  
  To unsubscribe from further messages, please visit
  https://sourceforge.net/auth/subscriptions/
  
  Related
  
  Issues: #400
  
  alternate
  
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  - sjoemac - 2016-06-25
    
    Wasn't easy, but merge is done. Xlink Code will need to be debugged esp
    with the inclusion of mods.
    
    Sean
    
    On Fri, Jun 24, 2016 at 1:11 PM, William S Noble wsnoble@users.sf.net
    wrote:
    
    Crud, you are right -- I just verified this. Apparently, the behavior only
    appears in the crux-sfx-topn branch. Sean, what is the feasibility of
    merging from the trunk into your branch, now that the mods handling is all
    fixed?
    
    Bill
    
    On Fri, Jun 24, 2016 at 11:02 AM, Kaipo kaipot@users.sf.net wrote:
    
    Actually, I made a fix for this and went to test it but I tried running
    it
    without the fix and I didn't get any error with either mstoolkit or
    proteowizard.
    
    [issues:#400] https://sourceforge.net/p/cruxtoolkit/issues/400/
    tide-search fails to parse MGF file*
    
    Status: open
    Milestone: post v2.0
    Labels: High priority
    Created: Wed Jun 22, 2016 07:13 PM UTC by William S Noble
    Last Updated: Wed Jun 22, 2016 08:52 PM UTC
    Owner: Kaipo
    Attachments:
    
    small.mgf
    <
    https://sourceforge.net/p/cruxtoolkit/issues/400/attachment/small.mgf>
    (274.9 kB; application/octet-stream)
    
    The tide-search command fails to parse the attached MGF file,
    irrespective
    of whether I use the pwiz or mstoolkit parser. In one case, it complains
    that it can't identify the format; in the other it complains about the
    line
    specifying the charge state.
    
    Here is a description of MGF:
    
    http://www.matrixscience.com/help/data_file_help.html
    
    I can't see any problem with the file I'm using.
    
    bash-4.1$ rm -fr crux-output;
    
    /net/noble/vol1/home/noble/proj/crux/branches/crux-sfx-topn/Debug/src/crux
    tide-search small.mgf
    ~peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
    INFO: Creating index from
    
    '/net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta'
    INFO: Running tide-index...
    INFO: Writing results to output directory
    'crux-output/tide-search.tempindex'.
    INFO: Reading
    
    /net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
    and computing unmodified peptides...
    INFO: Writing decoy fasta...
    INFO: Reading proteins
    INFO: Precomputing theoretical spectra...
    INFO: Beginning tide-search.
    WARNING: The output directory 'crux-output' already exists.
    Existing files will not be overwritten.
    INFO: CPU: pyrrolysine.gs.washington.edu
    INFO: Wed Jun 22 12:09:42 PDT 2016
    INFO: Running tide-search...
    INFO: Reading index crux-output/tide-search.tempindex
    INFO: Converting small.mgf to spectrumrecords format
    ERROR: [SpectrumList_MGF::parseSpectrum] Error parsing line at offset
    122: CHARGE=3+
    
    FATAL: Error converting small.mgf to spectrumrecords format
    bash-4.1$ rm -fr crux-output ;
    
    /net/noble/vol1/home/noble/proj/crux/branches/crux-sfx-topn/Debug/src/crux
    tide-search --spectrum-parser mstoolkit small.mgf
    ~peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
    INFO: Creating index from
    
    '/net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta'
    INFO: Running tide-index...
    INFO: Writing results to output directory
    'crux-output/tide-search.tempindex'.
    INFO: Reading
    
    /net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
    and computing unmodified peptides...
    INFO: Writing decoy fasta...
    INFO: Reading proteins
    INFO: Precomputing theoretical spectra...
    INFO: Beginning tide-search.
    WARNING: The output directory 'crux-output' already exists.
    Existing files will not be overwritten.
    INFO: CPU: pyrrolysine.gs.washington.edu
    INFO: Wed Jun 22 12:10:10 PDT 2016
    INFO: Running tide-search...
    INFO: Reading index crux-output/tide-search.tempindex
    INFO: Converting small.mgf to spectrumrecords format
    Unknown file format
    FATAL: MSToolkit: Error reading spectra file:
    
    /net/noble/vol4/noble/user/noble/proj/crux-projects/2016gaussian/results/bill/2016-06-22segfault/small.mgf
    
    Sent from sourceforge.net because you indicated interest in
    https://sourceforge.net/p/cruxtoolkit/issues/400/
    
    To unsubscribe from further messages, please visit
    https://sourceforge.net/auth/subscriptions/
    
    ** [issues:#400] tide-search fails to parse MGF file**
    
    Status: open
    Milestone: post v2.0
    Labels: High priority
    Created: Wed Jun 22, 2016 07:13 PM UTC by William S Noble
    Last Updated: Fri Jun 24, 2016 06:02 PM UTC
    Owner: Kaipo
    Attachments:
    
    small.mgf (sourceforge.net)
    (274.9 kB; application/octet-stream)
    
    The tide-search command fails to parse the attached MGF file, irrespective
    of whether I use the pwiz or mstoolkit parser. In one case, it complains
    that it can't identify the format; in the other it complains about the line
    specifying the charge state.
    
    Here is a description of MGF:
    
    http://www.matrixscience.com/help/data_file_help.html
    
    I can't see any problem with the file I'm using.
    
    bash-4.1$ rm -fr crux-output;
    /net/noble/vol1/home/noble/proj/crux/branches/crux-sfx-topn/Debug/src/crux
    tide-search small.mgf
    ~peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
    INFO: Creating index from
    '/net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta'
    INFO: Running tide-index...
    INFO: Writing results to output directory
    'crux-output/tide-search.tempindex'.
    INFO: Reading
    /net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
    and computing unmodified peptides...
    INFO: Writing decoy fasta...
    INFO: Reading proteins
    INFO: Precomputing theoretical spectra...
    INFO: Beginning tide-search.
    WARNING: The output directory 'crux-output' already exists.
    Existing files will not be overwritten.
    INFO: CPU: pyrrolysine.gs.washington.edu
    INFO: Wed Jun 22 12:09:42 PDT 2016
    INFO: Running tide-search...
    INFO: Reading index crux-output/tide-search.tempindex
    INFO: Converting small.mgf to spectrumrecords format
    ERROR: [SpectrumList_MGF::parseSpectrum] Error parsing line at offset 122:
    CHARGE=3+
    
    FATAL: Error converting small.mgf to spectrumrecords format
    bash-4.1$ rm -fr crux-output ;
    /net/noble/vol1/home/noble/proj/crux/branches/crux-sfx-topn/Debug/src/crux
    tide-search --spectrum-parser mstoolkit small.mgf
    ~peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
    INFO: Creating index from
    '/net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta'
    INFO: Running tide-index...
    INFO: Writing results to output directory
    'crux-output/tide-search.tempindex'.
    INFO: Reading
    /net/noble/vol1/home/peaklist/proj/data/crosslink/ribosome/ecoli_K12_ribo_02.fasta
    and computing unmodified peptides...
    INFO: Writing decoy fasta...
    INFO: Reading proteins
    INFO: Precomputing theoretical spectra...
    INFO: Beginning tide-search.
    WARNING: The output directory 'crux-output' already exists.
    Existing files will not be overwritten.
    INFO: CPU: pyrrolysine.gs.washington.edu
    INFO: Wed Jun 22 12:10:10 PDT 2016
    INFO: Running tide-search...
    INFO: Reading index crux-output/tide-search.tempindex
    INFO: Converting small.mgf to spectrumrecords format
    Unknown file format
    FATAL: MSToolkit: Error reading spectra file:
    /net/noble/vol4/noble/user/noble/proj/crux-projects/2016gaussian/results/bill/2016-06-22segfault/small.mgf
    
    Sent from sourceforge.net because you indicated interest in <
    https://sourceforge.net/p/cruxtoolkit/issues/400/>
    
    To unsubscribe from further messages, please visit <
    https://sourceforge.net/auth/subscriptions/>
    
    If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

William S Noble - 2016-09-07

labels: High priority -->

summary: tide-search fails to parse MGF file --> tide-search fails to parse MGF file (in search-for-xlinks branch)
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tide-search fails to parse MGF file (in search-for-xlinks branch)

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#400 tide-search fails to parse MGF file (in search-for-xlinks branch)

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