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] > <javascript:>> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <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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