Hi Jimmy,
thank you for your advice. I followed your advice and test the files one by one
and figured out one raw file name is different from the sequest search file
name (my colleague renamed the sequest search result file name). After I
renamed the raw file name to match the sequest results name. then the analyze
peptide went through without any problem.
The new problem is: when I click the peptide to check the xpress ratio
infomration or ms/ms informatin, there is error information showed below. Could
you give me some advice for this error information?
Thank you so much and have a nice weekend
Eileen
________________________________________
for ms/ms information erro:
command "c:\Inetpub\wwwroot\..\tpp-bin\tar.exe -tzf
c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_1
4-D_100ug_PierceIMAC_75um_140_20130423_VE2.tgz "*MAY1335_Yeast_1
4-D_100ug_PierceIMAC_75um_140_20130423_VE2.22310.22310.3.dta" > /dev/null"
failed: Operation not permitted Error - cannot read spectrum; tried direct
.dta, from mzXML/mzData and from .tgz
for xpress information error:
Light scans: mass: tol:
Heavy scans: mass: Z:
Raw file:
.out file: Norm:
Error - cannot open file
"c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_1".
----------------------------------------------------------------------------------------------------------------------------------------
From: [email protected] [[email protected]] On
Behalf Of Jimmy Eng [[email protected]]
Sent: Thursday, May 02, 2013 9:16 AM
To: [email protected]
Subject: Re: [spctools-discuss] why I got this error information?
Eileen,
The "+" in the file names is not a problem at this stage of processing although
it is a reserved character for a URL so you will have issues visualizing
results in the web interface. The "-" character is OK. For future reference,
it's not enough to simply change the pep.xml and mzML file names. You will
have to also make the corresponding changes to the content within the pep.xml
file, specifically the "base_name" attributes. I always suggest that
researchers stick to numbers, letters, dash "-", and underscore "_" in naming
files.
For your specific error, does the following file exist?
c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.mzML
If yes, I couldn't tell you why XPRESS is reporting that error. I would
suggest you try this analysis with just a single input file first to confirm
you can run the tools to completion. If that works, try this processing this
one MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.mzML file by itself.
- Jimmy
On Wed, May 1, 2013 at 1:27 PM, Eileen Yue
<[email protected]<mailto:[email protected]>> wrote:
Hello everyone.
I have one error information when I tried to analyze peptide for SILAC data. I
do not know whether this is possibly caused by file's name which includes "+"
and "-" . I did manually change the pep.xml and mzml files's name (which I
deleted "+" and "-" ) but I still get error information. Could anyone give me
some advice about this issue?
Thanks
Eileen
XPRESS error - cannot open file from basename
c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2,
will try to derive from scan names
command "C:/Inetpub/tpp-bin/XPressPeptideParser "interact.pep.xml" -m1 -nK,8
-nR,10 -c6 -p1" failed: Unknown error
command "C:/Inetpub/tpp-bin/XPressPeptideParser "interact.pep.xml" -m1 -nK,8
-nR,10 -c6 -p1" exited with non-zero exit code: -1073741819
QUIT - the job is incomplete
command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.75 -l6 -Op -dREV
-X-m1-nK,8-nR,10-c6-p1 -A-lKR-r0.5
MAY1335_Yeast_1+4-D_100ug_IMAC_75um_140_20130410_VE2.pep.xml
MAY1335_Yeast_1+4-D_100ug_POLY-Ti_75um_140_20130410_VE2.pep.xml
MAY1335_Yeast_1+4-D_100ug_PierceIMAC_75um_140_20130423_VE2.pep.xml
MAY1335_Yeast_2+3-D_100ug_IMAC_75um_140_20130410_VE2.pep.xml
MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.pep.xml
MAY1335_Yeast_2+3-D_100ug_POLY-Ti_75um_140_20130410_VE2.pep.xml" failed:
Unknown error
Command FAILED
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