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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