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 <shu...@stanford.edu > <javascript:>> 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 <shu...@stanford.edu> >>> 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 spctools-discu...@googlegroups.com. >>>> To post to this group, send email to spctools...@googlegroups.com. >>>> 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 spctools-discu...@googlegroups.com <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> 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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