Update: installing the new version of TPP, rather than addressing the memory issue (which may indeed have been a problem in the old TPP), solved the problem. Thanks!
On Tuesday, October 17, 2017 at 1:58:41 PM UTC-7, Steven Shuken wrote: > > Hi Jimmy, > > Interesting. I have decided to take someone else's advice to install a > newer version of TPP which installation is causing its own problems. If I > run into this problem again I will definitely consider the memory issue. > > Thanks, > Steven > > On Tuesday, October 17, 2017 at 1:00:51 PM UTC-7, Jimmy Eng wrote: >> >> The X!Tandem searches "ended" fast because they were terminated >> prematurely. Likely due to running out of memory. But if you have info >> which leads you to believe that memory is not the issue, I won't belabor >> the point. Good luck. >> >> On Tue, Oct 17, 2017 at 6:53 AM, Steven Shuken <[email protected]> >> wrote: >> >>> The computer has 16 GB of RAM. It is a lot but I don't mind the search >>> running for a few days as long as it runs. I don't think memory was the >>> issue because the searches ended so fast and the comet search is running >>> fine. I need the X!Tandem search to run. >>> >>> Thanks! >>> >>> On Monday, October 16, 2017 at 10:53:21 PM UTC-7, Jimmy Eng wrote: >>>> >>>> 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. >>> 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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