Hello, I'll take a look at the code this afternoon, but just for starters: can you verify that your mzXML files have a valid index? Looking up spectra without the aid of an index will considerably slow down Libra and other tools. Cheers, --Luis
On Apr 28, 2013, at 23:02, ChargedPeptide <[email protected]> wrote: > I've recently built TPP 4.6.2 on both Centos 6 and Ubuntu 12.1/13.04. > In all cases I have the same problem, the librapeptideparser step takes > literally forever (36 hours and counting) when processing itraq-data. > I've ran this exact workflow on TPP-4.5.2 on a windows box and > LibraPeptideParser would take minutes while the bulk of time would be spent > processing LibraProteinRatioParser, > though never more than an hour (and that is on a very slow box). > Since LibraPeptideParser gives NO output it is impossible to tell what is > going on, are there any logs generated by this?. > If any (devs especially) have any ides, know a global variable that needs to > be set or ANYTHING else about this it'd be appreciated. > The mzxml files are converted by msconvert from mgf files output by mascot > distiller. > Below is XInteract output for a test run of two files, though probably only > the last lin: > > > running: "/home/erik/tpp/bin/PeptideProphetParser > '/home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep.xml' > MINPROB=0.05 DECOY=dc ACCMASS" > using Accurate Mass Bins > Using Decoy Label "dc". > (X! Tandem (k-score)) > adding Accurate Mass mixture distr > init with X! Tandem (k-score) trypsin > MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: > UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN > > PeptideProphet (TPP v4.6 OCCUPY rev 2, Build 201304281953 (linux)) > AKeller@ISB > read in 42 1+, 6239 2+, 2220 3+, 1566 4+, 0 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > Found 3290 Decoys, and 6777 Non-Decoys > Iterations: .........10.........20....... > model complete after 28 iterations > command completed in 16 sec > > running: "/home/erik/tpp/bin/ProphetModels.pl -i > /home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep.xml -d dc" > Analyzing > /home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep.xml ... > Reading Accurate Mass Model model +1 ... > Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading > configurations from ~/.fonts.conf is deprecated. > Reading Accurate Mass Model model +2 ... > Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading > configurations from ~/.fonts.conf is deprecated. > Reading Accurate Mass Model model +3 ... > Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading > configurations from ~/.fonts.conf is deprecated. > Reading Accurate Mass Model model +4 ... > Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading > configurations from ~/.fonts.conf is deprecated. > Reading Accurate Mass Model model +5 ... > Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading > configurations from ~/.fonts.conf is deprecated. > Reading Accurate Mass Model model +6 ... > Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading > configurations from ~/.fonts.conf is deprecated. > Reading Accurate Mass Model model +7 ... > Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading > configurations from ~/.fonts.conf is deprecated. > Parsing search results > "/home/erik/tpp/data/taskController/LibraAllStepsConvert288e7eb159962475699b2a37526bbc8f9/MsConvertplugin/40a1ad168ae341b088edbe0233d45042/output/Batch2SaproItraqFrac100mMa > (X! Tandem (k-score))"... > => Total of 2057 hits. > => Total of 0 decoy hits. > => Total of 0 excluded hits. > Parsing search results > "/home/erik/tpp/data/taskController/LibraAllStepsConvert288e7eb159962475699b2a37526bbc8f9/MsConvertplugin/40a1ad168ae341b088edbe0233d45042/output/Batch2SaproItraqFrac100mMb > (X! Tandem (k-score))"... > => Total of 3601 hits. > => Total of 0 decoy hits. > => Total of 0 excluded hits. > Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading > configurations from ~/.fonts.conf is deprecated. > Warning: empty y range [0:0], adjusting to [0:1] > > plot > "/home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep_FVAL.tsv" > using 1:17 title "Observed" with line lc -1 , > "/home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep_FVAL.tsv" > using 1:18 title "Model Pos" with line lc 3 , > "/home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep_FVAL.tsv" > using 1:19 title "Model Neg" with line lc 1 > > ^ > "/home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep_FVAL.gp", > line 23: warning: Skipping data file with no valid points > Warning: empty y range [0:0], adjusting to [0:1] > > plot > "/home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep_FVAL.tsv" > using 1:20 title "Observed" with line lc -1 , > "/home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep_FVAL.tsv" > using 1:21 title "Model Pos" with line lc 3 , > "/home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep_FVAL.tsv" > using 1:22 title "Model Neg" with line lc 1 > > ^ > "/home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep_FVAL.gp", > line 25: warning: Skipping data file with no valid points > Warning: empty y range [0:0], adjusting to [0:1] > Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading > configurations from ~/.fonts.conf is deprecated. > Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading > configurations from ~/.fonts.conf is deprecated. > command completed in 2 sec > > running: "/home/erik/tpp/bin/LibraPeptideParser > '/home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/interact.pep.xml' > -c/home/erik/tpp/tmp/6c80b7f63abd436295d2ec4b65277194/condition.xml" > > -- > 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. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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