Hi,
I can't make attachment with my last email, so I send one more about
my error messages.
1. The data folder only contain one mzXML file and its mascot.dat file
(searched again used current SwissProt 57.12 database in our in-house
Mascot server) got:
c:/Inetpub/wwwroot/ISB/data/SSM4-1/F030337.pep.xml [ Unreadable! ]
run_in c:/Inetpub/wwwroot/ISB/data/SSM4-1; c:\Inetpub\tpp-bin
\Mascot2XML c:/Inetpub/wwwroot/ISB/data/SSM4-1/F030337.dat -Dc:/
Inetpub/wwwroot/ISB/data/SwissProt_57.12.fasta -Etrypsin
________________________________________
filepath: c:/Inetpub/wwwroot/ISB/data/SSM4-1/, extn: F030337
A stored as 71.0371
B stored as 114.535
C stored as 103.009
D stored as 115.027
E stored as 129.043
F stored as 147.068
G stored as 57.0215
H stored as 137.059
I stored as 113.084
J stored as 0
K stored as 128.095
L stored as 113.084
M stored as 131.04
N stored as 114.043
O stored as 0
P stored as 97.0528
Q stored as 128.059
R stored as 156.101
S stored as 87.032
T stored as 101.048
U stored as 150.954
V stored as 99.0684
W stored as 186.079
X stored as 111
Y stored as 163.063
Z stored as 128.551
c stored as 17.0027
n stored as 1.00782
variable modification 1, delta mass 227.127 for ICAT-C (C):
residues: C
nterm: 0
cterm: 0
protterm: 0
variable modification 2, delta mass 236.157 for ICAT-C:13C(9) (C):
residues: C
nterm: 0
cterm: 0
protterm: 0
variable modification 3, delta mass 15.9949 for Oxidation (M):
residues: M
nterm: 0
cterm: 0
protterm: 0
trypsin : cut(KR) nocuts(P) sense(C)
command "c:\Inetpub\tpp-bin\Mascot2XML c:/Inetpub/wwwroot/ISB/data/
SSM4-1/F030337.dat -Dc:/Inetpub/wwwroot/ISB/data/SwissProt_57.12.fasta
-Etrypsin" failed: Operation not permitted
Command FAILED
2. The data fold contain one mzXML file and its Mascot.pepxml file. I
directly used “Analysis Pipeline (Mascot) / Analyze Peptides” got
c:/Inetpub/wwwroot/ISB/data/SSM_4_1/SSM4-1.pep.shtml [ View ]
run_in c:/Inetpub/wwwroot/ISB/data/SSM_4_1; c:\Inetpub\tpp-bin
\xinteract -NSSM4-1.pep.xml -p0.05 -l7 -Oi -X-m1.0-nC,9.0 -A-lC-r0.5
c:/Inetpub/wwwroot/ISB/data/SSM_4_1/F028529-2.xml
________________________________________
c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build
200909091257 (MinGW))
running: "C:/Inetpub/tpp-bin/InteractParser "SSM4-1.pep.xml" "c:/
Inetpub/wwwroot/ISB/data/SSM_4_1/F028529-2.xml" -L"7""
file 1: c:/Inetpub/wwwroot/ISB/data/SSM_4_1/F028529-2.xml
processed altogether 337 results
results written to file c:/Inetpub/wwwroot/ISB/data/SSM_4_1/
SSM4-1.pep.xml
direct your browser to http://localhost/ISB/data/SSM_4_1/SSM4-1.pep.shtml
command completed in 1 sec
running: "C:/Inetpub/tpp-bin/PeptideProphetParser "SSM4-1.pep.xml"
MINPROB=0.05 ICAT"
(MASCOT) (icat)
error: -1.0 ion score
command "C:/Inetpub/tpp-bin/PeptideProphetParser "SSM4-1.pep.xml"
MINPROB=0.05 ICAT" failed: Operation not permitted
command "C:/Inetpub/tpp-bin/PeptideProphetParser "SSM4-1.pep.xml"
MINPROB=0.05 ICAT" exited with non-zero exit code: 1
QUIT - the job is incomplete
command "c:\Inetpub\tpp-bin\xinteract -NSSM4-1.pep.xml -p0.05 -l7 -Oi -
X-m1.0-nC,9.0 -A-lC-r0.5 c:/Inetpub/wwwroot/ISB/data/SSM_4_1/
F028529-2.xml" failed: Operation not permitted
Command FAILED
3. The data fold contain one mzXML file and its Mascot.xml file. I
directly used “Analysis Pipeline (Mascot) / Analyze Peptides” got
c:/Inetpub/wwwroot/ISB/data/SSM_4_1/SSM4-1.pep.shtml [ View ]
CAN NOT open the pepxml viewer in TPP
run_in c:/Inetpub/wwwroot/ISB/data/SSM_4_1; c:\Inetpub\tpp-bin
\xinteract -NSSM4-1.pep.xml -p0.05 -l7 -Oi -X-m1.0-nC,9.0 -A-lC-r0.5
c:/Inetpub/wwwroot/ISB/data/SSM_4_1/F028529.xml
________________________________________
c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build
200909091257 (MinGW))
running: "C:/Inetpub/tpp-bin/InteractParser "SSM4-1.pep.xml" "c:/
Inetpub/wwwroot/ISB/data/SSM_4_1/F028529.xml" -L"7""
file 1: c:/Inetpub/wwwroot/ISB/data/SSM_4_1/F028529.xml
processed altogether 0 results
ERROR: output file created, c:/Inetpub/wwwroot/ISB/data/SSM_4_1/
SSM4-1.pep.xml, appears incomplete. Please check the input files for
completeness.
results written to file c:/Inetpub/wwwroot/ISB/data/SSM_4_1/
SSM4-1.pep.xml
direct your browser to http://localhost/ISB/data/SSM_4_1/SSM4-1.pep.shtml
command completed in 0 sec
running: "C:/Inetpub/tpp-bin/PeptideProphetParser "SSM4-1.pep.xml"
MINPROB=0.05 ICAT"
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
error: no peptideprophet data written to file SSM4-1.pep.xml
Error: file update failed, check file SSM4-1.pep.xml.tmp.a02524 for
completeness
command "C:/Inetpub/tpp-bin/PeptideProphetParser "SSM4-1.pep.xml"
MINPROB=0.05 ICAT" failed: Operation not permitted
command "C:/Inetpub/tpp-bin/PeptideProphetParser "SSM4-1.pep.xml"
MINPROB=0.05 ICAT" exited with non-zero exit code: 1
QUIT - the job is incomplete
command "c:\Inetpub\tpp-bin\xinteract -NSSM4-1.pep.xml -p0.05 -l7 -Oi -
X-m1.0-nC,9.0 -A-lC-r0.5 c:/Inetpub/wwwroot/ISB/data/SSM_4_1/
F028529.xml" failed: Operation not permitted
Command FAILED
Fay
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