Brian,
TPP v4.3.1 on Ubuntu 9.04 and Fedora Core 8. Servers are both 8 core
2.6Ghz Opteron/Zeon with 32Gb RAM or more, so no slow cpu/memory issues.
Having seen Jake's experience of the same slowness I've just compiled
the TPP with debug and profiling flags, and have used gperf to look at
the call tree on a much smaller file.
It looks like ASAPRatioGroupPeptideParser::parse is called for each
protein group in the prot.xml that has non zero probability. Each
invocation parses the entire .pep.xml to find the associated peptide
information. In our case there are 9936 non-zero probability protein
groups in the .prot.xml, and the .pep.xml is 1.3GB, so I'm not surprised
it's taking days now.
We're looking to quantitate some very large datasets, so I hopefully can
put some time to looking at this. Something along the lines of an
initial step parsing all quantitated peptides in the .pep.xml into a
hash table containing the required information comes to mind, so that
the .pep.xml only has to be looked at once. I'll look into this next week.
DT
Brian Pratt wrote:
That doesn't sound right, no. I'd expect ASAPRatioProteinRatioParser
to run faster than ASAPRatioPeptideRatioParser, not slower. What OS,
what TPP version, etc?
Brian Pratt
Insilicos
On Thu, Feb 4, 2010 at 8:15 AM, Dave Trudgian <[email protected]
<mailto:[email protected]>> wrote:
Hi,
I'm experiencing very long processing times for
ASAPRatioProteinRatioParser. On a large dataset (48 x 2 hr QTOF
runs, ~100K spectrum IDs) ASAPRatioPeptideRatioParser completes
within a couple of hours, but ASAPRatioProteinRatioParser is
taking days. I assumed that the the peptide quantitation would be
the slower step due to chromatogram extraction from the mzXML,
with the protein ratio creation only involving rolling these
ratios up to the protein level, but this appears not to be the case.
Just wondering whether the large disparity in run-time between the
PeptideRatio and ProteinRatio parsers is expected?
Thanks,
DT
--
Dr. David Trudgian
Bioinformatician in Proteomics
University of Oxford
Mon-Thu: CCMP, Roosevelt Drive
Tel: (+44) (01865 2)87784
Friday : Dunn School of Pathology, S. Parks Rd.
Tel: (+44) (01865 2)75557
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