Hi, Dear SPC users and developers:
I'm wondering if anyone have some clue or remedy to the problem I have with
the X!tandem search in TPP(v4.7.1):
I have some Orbitrap Velos data in RAW and converted them to mzXML files by
MSconverter (ProteoWizard).
I ran the Comet pipeline on them and everything was just fine.
However, when I search the same mzXMLs by Tandem, some of those files gave
error reports:
_________________________________________
X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB)
Loading spectra (mzParser)............................ loaded.
Spectra matching criteria = 55267
Pluggable scoring enabled.
Starting threads . started.
Computing models:
12345678
*********
Warning: One or more sequences appear to contain invalid amino acid codes.
*********
9 sequences modelled = 9 ks
Model refinement:
partial cleavage .......... done.
finishing refinement ... done.
Creating report:
initial calculations ..... done.
sorting ..... done.
finding repeats ..... done.
evaluating results ..... done.
calculating expectations ..... done.
writing results ..... done.
command "c:\Inetpub\tpp-bin\tandem
c:/Inetpub/wwwroot/ISB/data/xxx.tandem.params" failed: Unknown error
Command FAILED
RETURN CODE:65280
_________________________________________
Despite this error message, the .tandem files were generated,
When I use the command tandem2XML to convert the .tandem files to .pep.xml,
as expected, it didn't work out:
Operation not permitted
Command FAILED
RETURN CODE:256
It only happens in few mzXML files, not all of them. And Comet runs OK on
all files, so I guess the mzXMLs should be fine.
I further checked .tandem files, looks like they contain all necessary
parts of Xtandem search results, and all spectra-peptide matches were
listed there with scores. I just don't know why such files still gave error
message and cannot go through tandem2XML.
Please help!
Thank you very much!
SunSun
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