Dear all,
I'm trying to run qualscore to retrieve any non-matching spectra for
re-matching against additional RNASeq-derived protein databases, however
qualscore doesn't output any spectra (and returns NaN coefficients) even
though it mentions there are unassigned spectra (15194) after the initial
search against canonical protein sequences.
These are the issued commands leading up to the problem:
- Converting mzML to mzXML
- msconvert
/home/job/mnt/dataProt/testData/1524_F_141114_005_hilic_pool_6_most_int.mzML
-o /home/job/outputProt/convertedInputFiles --filter "peakPicking true
1-"
--mzXML
- Running Comet against canonical + isoforms + decoys (decoy_ prefix)
- comet.exe -P/home/job/outputProt/phaseI/comet_phaseI.params
/home/job/outputProt/convertedInputFiles/1524_F_141114_005_hilic_pool_6_most_int.mzXML
- Running peptideProphet
- xinteract -Npeppro_1524_F_141114_005_hilic_pool_6_most_int.mzXML
-OAdP -p0 -ddecoy_ -EproteoRun
- Retrieving non-matched high-quality spectra :(
- java -jar -Xmx8096m qualscore_v1.0_2.jar -lp -c 1.0 -p 0.1
peppro_1524_F_ReneBraakman_141114_005_hilic_pool_6_most_int.pep.xml
It outputs the following:
> Picked up JAVA_TOOL_OPTIONS: -javaagent:/usr/share/java/jayatanaag.jar
> QualScore version 1.0_2 Copyright (C) 2006
> Institute for Systems Biology, Seattle WA
> QualScore is free software and comes with absolutely no warranty.
>
> XML
> Loading interact data:
> 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000
> 12000 13000 14000 15000 16000 17000 18000 19000 20000 21000
> 22000 23000 24000 25000 26000 27000 28000 29000 29678
> Interact data file contains 29677 entries.
> 0 +1 were removed.
> Enumerating scans:
> processing 1524_F_141114_005_hilic_pool_6_most_int.mzXML... 500 1000
> 1500 2000 2500 3000 3500 4000 4500 5000 5500 6000 6500 7000 7500 8000 8500
> 9000 9500 10000 10500 11000 11500 12000 12500 13000 13500 14000 14500 15000
> 15500 16000 16500 17000 17500 18000 18500 19000 19500 20000 20500 21000
> 21500 22000 22500 23000 23500 24000 24500 25000 25500 26000 26500 27000
> 27500 28000 28500 29000 29500 29677
> Features calculated for: 29677 (196903 ms)
> Training set: 12154/14148 (good/bad)
> Unassigned spectra: 15194
> Quality score calculation time: 162 ms
> Writing classifier co-efficients to file:
> peppro_1524_F_141114_005_hilic_pool_6_most_int.pep.xml.unassigned.qual.coef
> 0 spectra written to
> 'peppro_1524_F_141114_005_hilic_pool_6_most_int.pep.xml.unassigned.qual'.
> Time: 199
>
Viewing the ..qual.coef file shows all coefficients to be outputted as NaN.
Does anyone know a fix or alternate method to retrieve non-matching
high-quality spectra? (I could write a custom script that does this but I'd
rather not reinvent the wheel ;) )
Thanks for any help!
Kind regards,
Job
--
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.
For more options, visit https://groups.google.com/d/optout.
