Thanks Luis, I really appreciate that.
The problematic files contain this:
<index name="scan">
<offset id="0">984</offset>
<offset id="1">2463</offset>
<offset id="2">4091</offset>
and a lot of others, so the files seem to be indexed correctly.
Since my last post I've I've tried a windows install of TPP 4.6.2 and have
the exact same problem there.
I then built TPP4.5.2 on ubuntu 12.04 and that IS able to run the whole
process succesfully but only if starting over all the way back from
MSConvert.
So I took the MSConvert version from there, put it with the rest of TPP
4.6.2 and VIOLA, everything works.
So the data is definitley rubbing libraPeptideParser the wrong way but I
have no idea how.
I'd be happy to provide anything else you need.
I'm going to give TPP 4.6.1 a shot with my test-cases and see if I can at
least get a semi-modern experience.
Thanks for your work.
/Erik
I'm gonna give 4.6.1 a shot and
Den måndagen den 29:e april 2013 kl. 16:34:17 UTC+2 skrev Luis:
> 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] <javascript:>>
> 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"
>
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