Thanks to Jimmy and Luis. The '%' symbol was the issue. The user apparently named their mzXML files to contain that character, example: Experiment_1_enrich_50%.mzXML
By replacing '%' with '%25' I got lorikeet working. I will deal with this user now and prevent the issue in the future. Thanks guys! Damian On Monday, April 8, 2013 3:15:05 PM UTC-4, GATTACA wrote: > > Hi. > > I'm running TPP 4.6.2 on RHEL 6.4 (64bit) fully patched. > Users are having problems viewing spectra in this version with lorikeet. > > It doesn't happen for all data sets but generally speaking the older the > interact XML files are, the less likely they are to be viewable in lorikeet. > > If I click on the 'Ions2' link in a pepXML file I get a grey screen with > nothing in the window. Here is the URL for the page: > > http://111.111.111.111/tpp/cgi-bin/plot-msms-js.cgi?PrecursorMassType=1&FragmentMassType=0&PepMass=1331.6054&Pep=SLRPGTAEQDEK&Dta=/tpp.data/venky/UM_2013_1308.2013_03_05.091612/UM_2013_1308_50%/UM_2013_1308_50%.00028.00028.2.dta > > Nothing gets written to the error logs. The http access logs report this: > [08/Apr/2013:15:01:53 -0400] "GET > /tpp/cgi-bin/plot-msms-js.cgi?PrecursorMassType=1&FragmentMassType=0&PepMass=1331.6054&Pep=SLRPGTAEQDEK&Dta=/tpp.data/venky/UM_2013_1308.2013_03_05.091612/UM_2013_1308_50%/UM_2013_1308_50%.00028.00028.2.dta > > HTTP/1.1" 200 2138 > > Using the old Comet viewer at least generates an error on the browser: > Error - cannot get scan number from input file > /tpp.data/venky/UM_2013_1308.2013_03_05.091612/; unexpected dta name format > > The error logs for httpd also get something: > [Mon Apr 08 15:09:56 2013] [error] [client 111.111.111.111] script not > found or unable to stat: /usr/local/apps/tpp/cgi-bin/vbasrur, referer: > http://111.111.1.111/tpp/cgi-bin/PepXMLViewer.cgi?page=1&columns=Pprobability%2CGspectrum%2CSexpect%2CGions2%2CGpeptide%2CGprotein%2CGcalc_neutral_pep_mass%2CGions&displayState=columnsOptionsDiv&exportSpreadsheet=0&sortField2=Gspectrum&sortDir2=0&FmPprobability2=&FMPprobability2=&xmlFileName=%2Ftpp.data%2Fvbasrur%2FUM_2013_1308.2013_03_05.091612%2Finteract.pep.xml&perPage=50&sortField=Gspectrum&sortDir=0&highlightedPeptideText=&highlightedProteinText=&highlightedSpectrumText=&expandProteinList=condense&minimizeTableHeaders=yes&requiredAA=&requiredPeptideText=&requiredProteinText=&requiredSpectrumText=&FmGnum_tol_term=&FmShyperscore=&FMShyperscore=&FmSnextscore=&FMSnextscore=&FmSbscore=&FMSbscore=&FmSyscore=&FMSyscore=&FmSexpect=&FMSexpect=&FmPprobability=&FMPprobability=&jumpPage=1 > > > Any ideas for what's going on? > Thanks, > Damian > -- 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 http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
