How much RAM does your computer have? 158K spectra is a lot of spectra to load at once, especially using the k-score pluggable scoring option compared to native Tandem, so there's a chance that the program ran out of memory if you don't have lots of it on your machine. Monitor task manager while the search is running to see if this might be the problem.
Hopefully you've set "spectrum_batch_size" to some non-zero value in your Comet search. On Mon, Oct 16, 2017 at 9:17 PM, Steven Shuken <[email protected]> wrote: > Hello, > > I'm a grad student trying to put a SWATH library together. To learn how to > do this I looked up this paper by the Aebersold lab in 2015 which walks the > reader through the process: https://www.nature. > com/nprot/journal/v10/n3/full/nprot.2015.015.html > > I'm following the protocol which pointed me to download the X!Tandem > parameters below. Using these parameters, I get the error messages (farther > below) when trying to search the converted mzXML files using X!Tandem on > TPP. Any tips? I saw from a discussion in this group in 2013 that this may > be a parameter issue (Comet search has been running for hours but seems to > be working/hasn't given any errors) so I'll keep troubleshooting there. > Thanks! > > Parameters: > <?xml version="1.0"?> > <?xml-stylesheet type="text/xsl" href="tandem-input-style.xsl"?> > <bioml> > > <note>spectrum parameters</note> > <note type="input" label="spectrum, parent monoisotopic mass error > minus">50</note> > <note type="input" label="spectrum, parent monoisotopic mass error > plus">50</note> > <note>PRECURSOR MASS TOLERANCE. This is monoisotopic mass, so for > non-accurate-mass instruments, for which the precursor is often taken > nearer to the isotopically averaged mass, an asymmetric tolerance (-2.0 Da > to 4.0 Da) is preferable. This somewhat imitates a (-3.0 Da to 3.0 Da) > window for averaged mass (but not exactly).</note> > <note type="input" label="spectrum, parent monoisotopic mass isotope > error">no</note> > <note type="input" label="spectrum, fragment monoisotopic mass error > units">ppm</note> > <note>The value for this parameter may be 'Daltons' or 'ppm': all other > values are ignored</note> > <note type="input" label="spectrum, parent monoisotopic mass error > units">ppm</note> > <note>The value for this parameter may be 'Daltons' or 'ppm': all other > values are ignored</note> > <note type="input" label="spectrum, fragment monoisotopic mass > error">100</note> > <note>This parameter has no effect in k-score scoring.</note> > <note type="input" label="spectrum, fragment mass type">monoisotopic</note> > <note>values are monoisotopic|average </note> > > <note>spectrum conditioning parameters</note> > <note type="input" label="spectrum, use conditioning">no</note> > <note>For k-score scoring, it is recommended spectrum conditioning be > turned OFF for best performance. All of the spectrum filtering and > preprocessing options below in this section will be inactive.</note> > <note type="input" label="spectrum, dynamic range">10000.0</note> > <note type="input" label="spectrum, total peaks">400</note> > <note type="input" label="spectrum, maximum parent charge">5</note> > <note type="input" label="spectrum, use noise suppression">yes</note> > <note type="input" label="spectrum, minimum parent m+h">600.0</note> > <note type="input" label="spectrum, minimum fragment mz">125.0</note> > <note type="input" label="spectrum, minimum peaks">10</note> > <note type="input" label="spectrum, threads">1</note> > <note type="input" label="spectrum, sequence batch size">1000</note> > <note>residue modification parameters</note> > <note type="input" label="residue, modification mass">57.021464@C</note> > <note>STATIC MODIFICATION. The format of this parameter is m@X, where m > is the modfication mass in Daltons and X is the appropriate residue to > modify. Lists of modifications are separated by commas. For example, to > modify M and C with the addition of 16.0 Daltons, the parameter line would > be +16.0@M,+16.0@C. Positive and negative values are allowed.</note> > <note type="input" label="residue, potential modification mass">15.994915@M > </note> > <note>VARIABLE MODIFICATION. The format of this parameter is the same as > the format for residue, modification mass (see above).</note> > <note type="input" label="residue, potential modification motif"></note> > <note>VARIABLE MODIFICATION IN A MOTIF. The format of this parameter is > similar to residue, modification mass, with the addition of a modified > PROSITE notation sequence motif specification. For example, a value of > 80@[ST!]PX[KR] > indicates a modification of either S or T when followed by P, and residue > and the a K or an R. A value of 204@N!{P}[ST]{P} indicates a modification > of N by 204, if it is NOT followed by a P, then either an S or a T, NOT > followed by a P. Positive and negative values are allowed. </note> > > <note>protein parameters</note> > <note type="input" label="protein, taxon">no default</note> > <note>SEQUENCE DATABASE TO SEARCH. This refers to identifiers in > taxonomy.xml.</note> > <note type="input" label="protein, cleavage site">[RK]|{P}</note> > <note type="input" label="protein, cleavage semi">no</note> > <note>ENZYME SPECIFICITY. This setting corresponds to the enzyme trypsin. > The first characters in brackets represent residues N-terminal to the bond > - the '|' pipe - and the second set of characters represent residues > C-terminal to the bond. The characters must be in square brackets (denoting > that only these residues are allowed for a cleavage) or french brackets > (denoting that these residues cannot be in that position). Use UPPERCASE > characters. To denote cleavage at any residue, use [X]|[X] and reset the > scoring, maximum missed cleavage site parameter (see below) to something > like 50. </note> > <note type="input" label="protein, modified residue mass file"></note> > <note type="input" label="protein, N-terminal residue modification > mass"></note> > <note type="input" label="protein, C-terminal residue modification > mass"></note> > <note type="input" label="protein, homolog management">no</note> > <note>if yes, an upper limit is set on the number of homologues kept for a > particular spectrum</note> > <note type="input" label="protein, quick acetyl">no</note> > <note type="input" label="protein, quick pyrolidone">no</note> > > <note>model refinement parameters</note> > <note type="input" label="refine">no</note> > <note type="input" label="refine, modification mass"></note> > <note type="input" label="refine, sequence path"></note> > <note type="input" label="refine, tic percent">10</note> > <note type="input" label="refine, spectrum synthesis">yes</note> > <note type="input" label="refine, maximum valid expectation > value">0.1</note> > <note type="input" label="refine, potential N-terminus > modifications"></note> > <note type="input" label="refine, potential C-terminus > modifications"></note> > <note type="input" label="refine, unanticipated cleavage">no</note> > <note type="input" label="refine, potential modification mass"></note> > <note type="input" label="refine, point mutations">no</note> > <note type="input" label="refine, use potential modifications for full > refinement">no</note> > <note type="input" label="refine, point mutations">no</note> > <note type="input" label="refine, potential modification motif"></note> > > <note>scoring parameters</note> > > <note type="input" label="scoring, algorithm">k-score</note> > <note type="input" label="scoring, minimum ion count">4</note> > <note type="input" label="scoring, maximum missed cleavage sites">2</note> > <note type="input" label="scoring, x ions">no</note> > <note type="input" label="scoring, y ions">yes</note> > <note type="input" label="scoring, z ions">no</note> > <note type="input" label="scoring, a ions">no</note> > <note type="input" label="scoring, b ions">yes</note> > <note type="input" label="scoring, c ions">no</note> > <note type="input" label="scoring, cyclic permutation">no</note> > <note>if yes, cyclic peptide sequence permutation is used to pad the > scoring histograms</note> > <note type="input" label="scoring, include reverse">no</note> > <note>if yes, then reversed sequences are searched at the same time as > forward sequences</note> > <note type="input" label="scoring, cyclic permutation">no</note> > <note type="input" label="scoring, include reverse">no</note> > > <note>output parameters</note> > <note type="input" label="output, log path"></note> > <note type="input" label="output, message">1234567890</note> > <note type="input" label="output, sequence path"></note> > <note type="input" label="output, path">output.xml</note> > <note type="input" label="output, sort results by">spectrum</note> > <note>values = protein|spectrum (spectrum is the default)</note> > <note type="input" label="output, path hashing">no</note> > <note>values = yes|no</note> > <note type="input" label="output, xsl path">tandem-style.xsl</note> > <note type="input" label="output, parameters">yes</note> > <note>values = yes|no</note> > <note type="input" label="output, performance">yes</note> > <note>values = yes|no</note> > <note type="input" label="output, spectra">no</note> > <note>values = yes|no</note> > <note type="input" label="output, histograms">no</note> > <note>values = yes|no</note> > <note type="input" label="output, proteins">yes</note> > <note>values = yes|no</note> > <note type="input" label="output, sequences">no</note> > <note>values = yes|no</note> > <note type="input" label="output, one sequence copy">no</note> > <note>values = yes|no, set to yes to produce only one copy of each protein > sequence in the output xml</note> > <note type="input" label="output, results">all</note> > <note>values = all|valid|stochastic</note> > <note type="input" label="output, maximum valid expectation > value">0.1</note> > <note>value is used in the valid|stochastic setting of output, > results</note> > <note type="input" label="output, histogram column width">30</note> > <note>values any integer greater than 0. Setting this to '1' makes cutting > and pasting histograms into spread sheet programs easier.</note> > > <note type="description">ADDITIONAL EXPLANATIONS</note> > <note type="description">Each one of the parameters for X! tandem is > entered as a labeled note node. In the current version of X!, keep those > note nodes on a single line.</note> > <note type="description">The presence of the type 'input' is necessary if > a note is to be considered an input parameter. </note> > <note type="description">Any of the parameters that are paths to files may > require alteration for a particular installation. Full path names usually > cause the least trouble, but there is no reason not to use relative path > names, if that is the most convenient.</note> > <note type="description">Any parameter values set in the 'list path, > default parameters' file are reset by entries in the normal input file, if > they are present. Otherwise, the default set is used. </note> > <note type="description">The 'list path, taxonomy information' file must > exist.</note> > <note type="description">The directory containing the 'output, path' file > must exist: it will not be created.</note> > <note type="description">The 'output, xsl path' is optional: it is only of > use if a good XSLT style sheet exists.</note> > > </bioml> > > > > > Errors: > > Command 1 [Mon Oct 16 17:31:01 2017] [ Show / Hide ] > *EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem.params * > > X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB) > > Loading spectra > (mzParser)................................................................................ > loaded. > Spectra matching criteria = 158033 > Pluggable scoring enabled. > Starting threads . > This application has requested the Runtime to terminate it in an unusual way. > Please contact the application's support team for more information. > > command "c:\Inetpub\tpp-bin\tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem.params" failed: No > such process > > *Command FAILED* > RETURN CODE:768 > > Command 2 [Mon Oct 16 17:31:24 2017] [ Show / Hide ] > *EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; > c:\Inetpub\tpp-bin\Tandem2XML > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem.pep.xml * > > Failed to open input file > 'c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem'. > > command "c:\Inetpub\tpp-bin\Tandem2XML > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_001.tandem.pep.xml" failed: > Operation not permitted > > *Command FAILED* > RETURN CODE:256 > > Command 3 [Mon Oct 16 17:31:24 2017] [ Show / Hide ] > *EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem.params * > > X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB) > > Loading spectra > (mzParser)................................................................................ > loaded. > Spectra matching criteria = 158770 > Pluggable scoring enabled. > Starting threads . > This application has requested the Runtime to terminate it in an unusual way. > Please contact the application's support team for more information. > > command "c:\Inetpub\tpp-bin\tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem.params" failed: > Unknown error > > *Command FAILED* > RETURN CODE:65280 > > Command 4 [Mon Oct 16 17:31:48 2017] [ Show / Hide ] > *EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; > c:\Inetpub\tpp-bin\Tandem2XML > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem.pep.xml * > > Failed to open input file > 'c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem'. > > command "c:\Inetpub\tpp-bin\Tandem2XML > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_010.tandem.pep.xml" failed: > Operation not permitted > > *Command FAILED* > RETURN CODE:256 > > Command 5 [Mon Oct 16 17:31:48 2017] [ Show / Hide ] > *EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem.params * > > X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB) > > Loading spectra > (mzParser)................................................................................ > loaded. > Spectra matching criteria = 158289 > Pluggable scoring enabled. > Starting threads . > This application has requested the Runtime to terminate it in an unusual way. > Please contact the application's support team for more information. > > command "c:\Inetpub\tpp-bin\tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem.params" failed: > Unknown error > > *Command FAILED* > RETURN CODE:65280 > > Command 6 [Mon Oct 16 17:32:30 2017] [ Show / Hide ] > *EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; > c:\Inetpub\tpp-bin\Tandem2XML > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem.pep.xml * > > Failed to open input file > 'c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem'. > > command "c:\Inetpub\tpp-bin\Tandem2XML > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem > c:/Inetpub/wwwroot/ISB/data/nselevse_L120327_016.tandem.pep.xml" failed: > Operation not permitted > > *Command FAILED* > RETURN CODE:256 > > All commands finished at *Mon Oct 16 17:32:30 2017* > -Steven > > -- > 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. 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