Hello Jagan, I am not sure what steps you took to do the search but I've tracked the problem down to windows style line ending characters '^M' ending up in the tandem xml file that I downloaded jagan-J134.xml. They present at the end of every spectrum name in the <note label="Description"> tags. The new Tandem2XML tool has been changed and it inserts newlines in the pep.xml file where the downstream tools don't expect to see newlines and breaks the downstream parsing. To solve this problem please remove the offending characters from the spectrum names of any future files you generate (or figure out what step in your analysis is adding this character and adjust your pipeline) and the problem will go away. Your file with the characters removed is here http://groups.google.com/group/spctools-discuss/web/jagan-J134.xml.gz?hl=en Let me know if you still have any problems processing this file.
Cheers, -David On Wed, Jun 30, 2010 at 10:55 PM, Jagan Kommineni <[email protected]> wrote: > Dear All, > > I took standard search results of x!tandem (X! TANDEM 2009.10.01.1 > (LabKey and ISB). came from the release version of the TPP and run the > prophets both with Release version and Current Development version of the > TPP distribution and found the issues remain same as that of x!!tandem > search results. > > Release version returns hits but development version doesn't return any > results > > I suspect that there is something wrong either with the development > version prophet tools or it could be something wrong with input parameters > which has impact only on the development version of the TPP (prophets). > > Here are the pointers for the result files ... > > xtandem_search.zip(Standard Xtandem search input, result and log files) > TPPReleaseDebug.zip(xinteract run with release version and option "-t!") > TPPReleaseDevelopmentDebug.zip(xinteract run with development version and > option "-t#" after release version run with an option "-t!") > > Retrieved from > "https://search.apcf.edu.au/wiki/index.php/Apcfwiki:Community_Portal"; > > Any help is greatly appreciated. > > with regards, > > Jagan Kommineni > > > On Fri, Jun 25, 2010 at 1:49 PM, Jagan Kommineni <[email protected]> > wrote: >> >> Brian and David, >> >> I noticed similar failure messages when I run xitentct with release >> version and then current (development version as of 25-06-2010), here is the >> output, >> >> >> STDOUT message on the screen when run xinteract with todays development >> version of TPP with option "-t#" after running xitneract with release >> version of TPP with an option of -t!. >> >> Again I put the latest generated files on APCF wiki and here are the >> pointers to download. >> >> >> (https://search.apcf.edu.au/wiki/index.php/Apcfwiki:Community_Portal#APCF_Downloads) >> >> xinteractReleaseVersion.zip(xinteract run with release version and option >> "-t!") >> >> xinteractReleaseAndDevelopmentVersion.zip(xinteract run with development >> version and option "-t#" after release version run with an option "-t!") >> >> >> =========================================================================================================== >> [r...@apcf-hn3 2010-06-25]# /home/APCF/tpp/bin/xinteract -t# >> -Njagan-J82.pepprophet.xml -p0.05 -l7 -x20 -O jagan-J82.pep.xml >> >> /home/APCF/tpp/bin/xinteract (TPP v4.4 JETSTREAM (unstable development >> prerelease) rev 0, Build 201006251153 (linux)) >> performing regression test (# option in use, will continue in case of >> error)... >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser >> -t#-Njagan-J82.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J82.pep.xml >> 'jagan-J82.pepprophet.xml' 'jagan-J82.pep.xml' -L'7'" >> running regression test on basis file >> jagan-J82.pepprophet.xml.interactParser.-Njagan-J82.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J82.pep.xml.tagList >> file 1: jagan-J82.pep.xml >> processed altogether 3429 results >> >> >> results written to file >> /mnt/sanfs/APCF/results/tpp/2010-06-25/jagan-J82.pepprophet.shtml >> >> >> >> interactParser regression test success >> command completed in 1 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >> 'jagan-J82.pepprophet.xml' MINPROB=0.05 EXTRAITRS=20 >> -t#-Njagan-J82.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J82.pep.xml" >> running regression test on basis file >> jagan-J82.pepprophet.xml.peptideProphet.-Njagan-J82.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J82.pep.xml.tagList >> (X! Tandem (k-score)) >> init with X! Tandem (k-score) trypsin >> MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ Orbitrap, >> Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive >> detector >> >> PeptideProphet (TPP v4.4 JETSTREAM (unstable development prerelease) rev >> 0, Build 201006251153 (linux)) akel...@isb >> read in 1127 1+, 1355 2+, 361 3+, 54 4+, 0 5+, 0 6+, and 0 7+ spectra. >> Initialising statistical models ... >> negmean = -0.490485 >> negmean = -0.0225753 >> negmean = -0.520051 >> negmean = 0.801738 >> negmean = -0.2 >> negmean = -0.2 >> negmean = -0.2 >> Iterations: .........10.........20........ >> WARNING: Mixture model quality test failed for charge (1+). >> model complete after 29 iterations >> different tag count: 718 vs 19620 >> <error_point error="0.001" min_prob="0.998" num_corr="32" num_incorr="0"/> >> does not agree with expected value >> <error_point error="0.010" min_prob="0.96" num_corr="187" num_incorr="2"/> >> at "error" in tag #30 at line 30 >> regression test FAILURE in PeptideProphet (see file >> PeptideProphet.bad.tagList) >> command completed in 1 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProphetModels.pl -i >> jagan-J82.pepprophet.xml" >> Analyzing jagan-J82.pepprophet.xml ... >> Parsing search results "jagan-J81 (X! Tandem (k-score))"... >> => Total of 0 hits. >> Could not find/open font when opening font "arial", using internal >> non-scalable font >> Warning: empty y range [0:0], adjusting to [0:1] >> Could not find/open font when opening font "arial", using internal >> non-scalable font >> >> plot "jagan-J82.pepprophet_PPPROB.tsv" using 2:1 title "PeptideProphet" >> with line lc 2 , x notitle with line lt 0 lc -1 >> >> >> ^ >> "jagan-J82.pepprophet_PPPROB.gp", line 16: warning: Skipping data file >> with no valid points >> Could not find/open font when opening font "arial", using internal >> non-scalable font >> >> plot "jagan-J82.pepprophet_IPPROB.tsv" using 2:1 title "iProphet" with >> line lc 2 , x notitle with line lt 0 lc -1 >> >> >> ^ >> "jagan-J82.pepprophet_IPPROB.gp", line 16: warning: Skipping data file >> with no valid points >> command completed in 0 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/DatabaseParser >> 'jagan-J82.pepprophet.xml'" >> command completed in 0 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser >> 'jagan-J82.pepprophet.xml' >> '/home/APCF/databases/SwissProt/uniprot_sprot.fasta' >> -t#-Njagan-J82.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J82.pep.xml" >> running regression test on basis file >> jagan-J82.pepprophet.xml.RefreshParser.-Njagan-J82.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J82.pep.xml.tagList >> - Building Commentz-Walter keyword tree... - Searching the tree... >> - Linking duplicate entries... - Printing results... >> >> different tag count: 1 vs 2184 >> regression test FAILURE in RefreshParser (see file >> RefreshParser.bad.tagList) >> command completed in 3 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I >> /mnt/sanfs/APCF/results/tpp/2010-06-25/jagan-J82.pepprophet.xml" >> >> command "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I >> /mnt/sanfs/APCF/results/tpp/2010-06-25/jagan-J82.pepprophet.xml" exited with >> non-zero exit code: 11 >> QUIT - the job is incomplete >> [r...@apcf-hn3 2010-06-25]# >> >> ================================================================================================= >> >> On Fri, Jun 25, 2010 at 12:24 AM, Brian Pratt <[email protected]> >> wrote: >>> >>> OK, that shows us that everything is the same up to the PeptideProphet >>> step (so, it's not that the input to peptideProphet changed, it's that >>> peptideProphet changed). Perhaps David has some thoughts. >>> >>> Given that this is the development version some bumps are to be >>> expected. It's also a good idea to build from the latest source to see if >>> the problem has already been found and fixed. >>> >>> On Wed, Jun 23, 2010 at 8:12 PM, Jagan Kommineni >>> <[email protected]> wrote: >>>> >>>> Brian, >>>> >>>> I run xinteract on Release and developement versions of the TPP with >>>> debug option -t! and -t# respectively. >>>> >>>> ==================================================================================================== >>>> With Release version of the TPP tools .... >>>> >>>> /home/APCF/tpp/bin/xinteract -t! -Njagan-J78.pepprophet.xml -p0.05 -l7 >>>> -x20 -O jagan-J78.pep.xml >>>> All the results files including logs are kept on wiki page which can be >>>> downloaded using the following link ... >>>> >>>> >>>> https://search.apcf.edu.au/wiki/index.php/Apcfwiki:Community_Portal#APCF_Downloads >>>> cliking on "DevelopmentRun.zip(xinteract run with release version and >>>> option "-t!") >>>> >>>> ------------------------------------------------------------------------------------------------------------------------------------------------------------------ >>>> With developmental version of the TPP .... >>>> >>>> /home/APCF/tpp/bin/xinteract -t# -Njagan-J78.pepprophet.xml -p0.05 -l7 >>>> -x20 -O jagan-J78.pep.xml >>>> All the results files including logs are kept on wiki page which can be >>>> downloaded using the following link ... >>>> >>>> >>>> https://search.apcf.edu.au/wiki/index.php/Apcfwiki:Community_Portal#APCF_Downloads >>>> cliking on "ReleaseDevelopmentRun.zip(xinteract run with development >>>> version and option "-t#" after release version run with an option "-t!") >>>> >>>> >>>> =================================================================================================== >>>> The STDOUT of the latter run is as follows ... >>>> >>>> It looks like there are erros, the regression tests were FAILURED in >>>> PeptideProphet run and the PeptideProphet.bad.tagList etc also included in >>>> the zipped files. >>>> >>>> I wonder whether anyone has any idea about this problem. >>>> >>>> >>>> ------------------------------------------------------------------------------------------------------------------------------------------------------------------ >>>> >>>> [r...@apcf-hn3 2010-06-23]# /home/APCF/tpp/bin/xinteract -t# >>>> -Njagan-J78.pepprophet.xml -p0.05 -l7 -x20 -O jagan-J78.pep.xml >>>> >>>> /home/APCF/tpp/bin/xinteract (TPP v4.4 JETSTREAM (unstable development >>>> prerelease) rev 0, Build 201006041141 (linux)) >>>> performing regression test (# option in use, will continue in case of >>>> error)... >>>> >>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser >>>> -t#-Njagan-J78.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J78.pep.xml >>>> 'jagan-J78.pepprophet.xml' 'jagan-J78.pep.xml' -L'7'" >>>> running regression test on basis file >>>> jagan-J78.pepprophet.xml.interactParser.-Njagan-J78.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J78.pep.xml.tagList >>>> file 1: jagan-J78.pep.xml >>>> processed altogether 3429 results >>>> >>>> >>>> results written to file >>>> /mnt/sanfs/APCF/results/tpp/2010-06-23/jagan-J78.pepprophet.shtml >>>> >>>> >>>> >>>> interactParser regression test success >>>> command completed in 1 sec >>>> >>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >>>> 'jagan-J78.pepprophet.xml' MINPROB=0.05 EXTRAITRS=20 >>>> -t#-Njagan-J78.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J78.pep.xml" >>>> running regression test on basis file >>>> jagan-J78.pepprophet.xml.peptideProphet.-Njagan-J78.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J78.pep.xml.tagList >>>> (X! Tandem (k-score)) >>>> init with X! Tandem (k-score) trypsin >>>> MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ >>>> Orbitrap, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: >>>> inductive detector >>>> >>>> PeptideProphet (TPP v4.4 JETSTREAM (unstable development prerelease) >>>> rev 0, Build 201006041141 (linux)) akel...@isb >>>> read in 1127 1+, 1355 2+, 361 3+, 54 4+, 0 5+, 0 6+, and 0 7+ spectra. >>>> Initialising statistical models ... >>>> negmean = -0.490485 >>>> negmean = -0.0225753 >>>> negmean = -0.520051 >>>> negmean = 0.801738 >>>> negmean = -0.2 >>>> negmean = -0.2 >>>> negmean = -0.2 >>>> Iterations: .........10.........20........ >>>> WARNING: Mixture model quality test failed for charge (1+). >>>> model complete after 29 iterations >>>> different tag count: 718 vs 19620 >>>> <error_point error="0.001" min_prob="0.998" num_corr="32" >>>> num_incorr="0"/> >>>> does not agree with expected value >>>> <error_point error="0.010" min_prob="0.96" num_corr="187" >>>> num_incorr="2"/> >>>> at "error" in tag #30 at line 30 >>>> regression test FAILURE in PeptideProphet (see file >>>> PeptideProphet.bad.tagList) >>>> command completed in 0 sec >>>> >>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProphetModels.pl -i >>>> jagan-J78.pepprophet.xml" >>>> Analyzing jagan-J78.pepprophet.xml ... >>>> Parsing search results "jagan-J77 (X! Tandem (k-score))"... >>>> => Total of 0 hits. >>>> Could not find/open font when opening font "arial", using internal >>>> non-scalable font >>>> Warning: empty y range [0:0], adjusting to [0:1] >>>> Could not find/open font when opening font "arial", using internal >>>> non-scalable font >>>> >>>> plot "jagan-J78.pepprophet_PPPROB.tsv" using 2:1 title "PeptideProphet" >>>> with line lc 2 , x notitle with line lt 0 lc -1 >>>> >>>> >>>> ^ >>>> "jagan-J78.pepprophet_PPPROB.gp", line 16: warning: Skipping data file >>>> with no valid points >>>> Could not find/open font when opening font "arial", using internal >>>> non-scalable font >>>> >>>> plot "jagan-J78.pepprophet_IPPROB.tsv" using 2:1 title "iProphet" with >>>> line lc 2 , x notitle with line lt 0 lc -1 >>>> >>>> >>>> ^ >>>> "jagan-J78.pepprophet_IPPROB.gp", line 16: warning: Skipping data file >>>> with no valid points >>>> command completed in 1 sec >>>> >>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/DatabaseParser >>>> 'jagan-J78.pepprophet.xml'" >>>> command completed in 0 sec >>>> >>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser >>>> 'jagan-J78.pepprophet.xml' >>>> '/home/APCF/databases/SwissProt/uniprot_sprot.fasta' >>>> -t#-Njagan-J78.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J78.pep.xml" >>>> running regression test on basis file >>>> jagan-J78.pepprophet.xml.RefreshParser.-Njagan-J78.pepprophet.xml_-p0.05_-l7_-x20_-O_jagan-J78.pep.xml.tagList >>>> - Building Commentz-Walter keyword tree... - Searching the tree... >>>> - Linking duplicate entries... - Printing results... >>>> >>>> different tag count: 1 vs 2184 >>>> regression test FAILURE in RefreshParser (see file >>>> RefreshParser.bad.tagList) >>>> command completed in 2 sec >>>> >>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I >>>> /mnt/sanfs/APCF/results/tpp/2010-06-23/jagan-J78.pepprophet.xml" >>>> >>>> command "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I >>>> /mnt/sanfs/APCF/results/tpp/2010-06-23/jagan-J78.pepprophet.xml" exited >>>> with >>>> non-zero exit code: 11 >>>> QUIT - the job is incomplete >>>> [r...@apcf-hn3 2010-06-23]# >>>> >>>> >>>> On Thu, Jun 24, 2010 at 1:39 AM, Brian Pratt <[email protected]> >>>> wrote: >>>>> >>>>> If you're running this using xinteract, you can debug a little by >>>>> adding "-t!" to the xinteract commandline on the release version, and >>>>> "-t#" >>>>> to the commandline for the development version. "-t!" (note the >>>>> exclamation >>>>> point) causes a series of test files to be generated (they're just copies >>>>> of >>>>> the output as the job progresses) and "-t#" causes the software to check >>>>> its >>>>> progress against those files. This may help you figure out where things >>>>> are >>>>> going wrong. >>>>> >>>>> On Wed, Jun 23, 2010 at 12:28 AM, Jagan Kommineni >>>>> <[email protected]> wrote: >>>>>> >>>>>> Dear All, >>>>>> >>>>>> When I run the TPP pipeline with downloaded version of the >>>>>> development prerelease of TPP dated 22-04-2010, I am getting 0 hits >>>>>> whereas when I run pipeline with release version of TPP (TPP v4.3 >>>>>> (jetstream) rev 1) for the same data and parameters, I am getting 822 >>>>>> hits. >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------------------------------------------------------------------------------------------ >>>>>> Here is the STDOUT when I run the TPP pipeline with >>>>>> development version downloaded on 22-04-2010 >>>>>> >>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- >>>>>> /home/APCF/tpp/bin/xinteract (TPP v4.4 JETSTREAM (unstable development >>>>>> prerelease) rev 0, Build 201006041141 (linux)) >>>>>> >>>>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser 'jagan- >>>>>> J78.pepprophet.xml' 'jagan-J78.pep.xml' -L'7'" >>>>>> >>>>>> file 1: jagan-J78.pep.xml >>>>>> >>>>>> processed altogether 3429 results >>>>>> >>>>>> results written to file /mnt/sanfs/APCF/results/tpp/2010-06-23/jagan- >>>>>> J78.pepprophet.shtml >>>>>> >>>>>> command completed in 1 sec >>>>>> >>>>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >>>>>> 'jagan- >>>>>> J78.pepprophet.xml' MINPROB=0.05 EXTRAITRS=20" >>>>>> >>>>>> (X! Tandem (k-score)) >>>>>> >>>>>> init with X! Tandem (k-score) trypsin >>>>>> >>>>>> MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ >>>>>> Orbitrap, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: >>>>>> inductive detector >>>>>> >>>>>> Initialising statistical models ... >>>>>> >>>>>> Iterations: .........10.........20........ >>>>>> >>>>>> model complete after 29 iterations >>>>>> >>>>>> command completed in 0 sec >>>>>> >>>>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProphetModels.pl -i jagan- >>>>>> J78.pepprophet.xml" >>>>>> >>>>>> Analyzing jagan-J78.pepprophet.xml ... >>>>>> >>>>>> Parsing search results "jagan-J77 (X! Tandem (k-score))"... >>>>>> >>>>>> => Total of 0 hits. >>>>>> >>>>>> command completed in 0 sec >>>>>> >>>>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/DatabaseParser 'jagan- >>>>>> J78.pepprophet.xml'" >>>>>> >>>>>> command completed in 0 sec >>>>>> >>>>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser 'jagan- >>>>>> J78.pepprophet.xml' '/home/APCF/databases/SwissProt/ >>>>>> uniprot_sprot.fasta'" >>>>>> >>>>>> - Searching the tree... >>>>>> >>>>>> - Linking duplicate entries... - Printing results... >>>>>> >>>>>> command completed in 3 sec >>>>>> >>>>>> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I / >>>>>> mnt/sanfs/APCF/results/tpp/2010-06-23/jagan-J78.pepprophet.xml" >>>>>> >>>>>> command "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I >>>>>> /mnt/ >>>>>> sanfs/APCF/results/tpp/2010-06-23/jagan-J78.pepprophet.xml" exited >>>>>> with non-zero exit code: 11 >>>>>> >>>>>> QUIT - the job is incomplete >>>>>> >>>>>> ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the >>>>>> original Perl by A. Keller (TPP v4.4 JETSTREAM (unstable development >>>>>> prerelease) rev 0, Build 201006041141 (linux)) >>>>>> >>>>>> (xml input) (report Protein Length) (using degen pep info) >>>>>> >>>>>> . . . reading in /mnt/sanfs/APCF/results/tpp/2010-06-23/jagan- >>>>>> J78.pepprophet.xml. . . >>>>>> >>>>>> did not find any PeptideProphet results in input data! Did you forget >>>>>> to run PeptideProphet? >>>>>> >>>>>> . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with >>>>>> min prob 0.05 >>>>>> >>>>>> no data - quitting >>>>>> >>>>>> ============================================================================== >>>>>> But when I run the same thing with release version of TPP (TPP v4.3 >>>>>> (jetstream) rev 1) everything went OK. >>>>>> Here is the STDOUT message .... >>>>>> >>>>>> --------------------------------------------------------------------------------------------------------------------------------------------------------------- >>>>>> >>>>>> [r...@compute-3-0 temp]# pwd >>>>>> /mnt/sanfs/APCF/results/tpp/2010-06-23/temp >>>>>> [r...@compute-3-0 temp]# ls >>>>>> jagan-J77.mzXML jagan-J77.xml >>>>>> [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ >>>>>> build/linux/Tandem2XML jagan-J77.xml jagan-J78.pep.xml >>>>>> [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ >>>>>> build/linux/InteractParser jagan-J78.pepprophet.xml jagan-J78.pep.xml >>>>>> - >>>>>> L7 >>>>>> file 1: jagan-J78.pep.xml >>>>>> processed altogether 3429 results >>>>>> >>>>>> results written to file /mnt/sanfs/APCF/results/tpp/2010-06-23/temp/ >>>>>> jagan-J78.pepprophet.shtml >>>>>> >>>>>> [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ >>>>>> build/linux/PeptideProphetParser jagan-J78.pepprophet.xml MINPROB=0.05 >>>>>> EXTRAITRS=20 >>>>>> (X! Tandem (k-score)) >>>>>> init with X! Tandem (k-score) trypsin >>>>>> MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ >>>>>> Orbitrap, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: >>>>>> inductive detector >>>>>> >>>>>> PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 201003241044 >>>>>> (linux)) akel...@isb >>>>>> read in 1127 1+, 1355 2+, 361 3+, 54 4+, 0 5+, 0 6+, and 0 7+ >>>>>> spectra. >>>>>> Initialising statistical models ... >>>>>> negmean = -0.490485 >>>>>> negmean = -0.0225753 >>>>>> negmean = -0.520051 >>>>>> negmean = 0.801738 >>>>>> negmean = -0.2 >>>>>> negmean = -0.2 >>>>>> negmean = -0.2 >>>>>> Iterations: .........10.........20........ >>>>>> WARNING: Mixture model quality test failed for charge (1+). >>>>>> model complete after 29 iterations >>>>>> [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ >>>>>> build/linux/ProphetModels.pl -i jagan-J78.pepprophet.xml >>>>>> Analyzing jagan-J78.pepprophet.xml ... >>>>>> Parsing search results "jagan-J77 (X! Tandem (k-score))"... >>>>>> => Total of 822 hits. >>>>>> [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ >>>>>> build/linux/DatabaseParser jagan-J78.pepprophet.xml >>>>>> /home/APCF/databases/SwissProt/uniprot_sprot.fasta >>>>>> [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ >>>>>> build/linux/RefreshParser jagan-J78.pepprophet.xml /home/APCF/ >>>>>> databases/SwissProt/uniprot_sprot.fasta >>>>>> - Building Commentz-Walter keyword tree... - Searching the tree... >>>>>> - Linking duplicate entries... - Printing results... >>>>>> [r...@compute-3-0 temp]# >>>>>> >>>>>> ============================================================================== >>>>>> >>>>>> I wonder whether there is any quick fix to this problem. Something >>>>>> broken from the release version to development version. >>>>>> >>>>>> with regards, >>>>>> >>>>>> Jagan Kommineni >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "spctools-discuss" group. >>>>>> To post to this group, send email to >>>>>> [email protected]. >>>>>> To unsubscribe from this group, send email to >>>>>> [email protected]. >>>>>> For more options, visit this group at >>>>>> http://groups.google.com/group/spctools-discuss?hl=en. >>>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "spctools-discuss" group. >>>>> To post to this group, send email to [email protected]. >>>>> To unsubscribe from this group, send email to >>>>> [email protected]. >>>>> For more options, visit this group at >>>>> http://groups.google.com/group/spctools-discuss?hl=en. >>>> >>>> >>>> >>>> -- >>>> Dr. Jagan Kommineni >>>> Ludwig Institute for Cancer research >>>> Pakville VIC 3145 >>>> Australia. >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To post to this group, send email to [email protected]. >>>> To unsubscribe from this group, send email to >>>> [email protected]. >>>> For more options, visit this group at >>>> http://groups.google.com/group/spctools-discuss?hl=en. >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "spctools-discuss" group. >>> To post to this group, send email to [email protected]. >>> To unsubscribe from this group, send email to >>> [email protected]. >>> For more options, visit this group at >>> http://groups.google.com/group/spctools-discuss?hl=en. >> >> >> >> -- >> Dr. Jagan Kommineni >> Ludwig Institute for Cancer research >> Pakville VIC 3145 >> Australia. > > > > -- > Dr. Jagan Kommineni > Ludwig Institute for Cancer research > Pakville VIC 3145 > Australia. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
