Hello Steven, It appears that you are using a very old version of the TPP. I wonder if you can test the latest version.
Thanks, -David 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.co >>> m/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. 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.
