Dear all,
I tried to run SEQUEST on a 1.5 GB RAW file on Windows via TPP. After
converting the RAW file to mzXML and after converting the mzXML to dta
files, however, the program crashes, presumably while trying to chmod
a file which is not there (maybe the path to the mzXML file is
missing?)...
Any help would be appreciated, thanks in advance!
The remainder of this message is the directory contents of the TPP
data directory and the TPP output.
C:\Inetpub\wwwroot\ISB\data>dir
Volume in drive C has no label.
Volume Serial Number is D85D-D9C9
Directory of C:\Inetpub\wwwroot\ISB\data
05/20/2009 03:19 PM <DIR> .
05/20/2009 03:19 PM <DIR> ..
05/20/2009 02:37 PM <DIR>
BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409
05/20/2009 02:26 PM 1,882,388,081
BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML.gz
04/25/2009 03:24 AM 1,467,652,494
BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.RAW
05/20/2009 10:50 AM <DIR> dbase
05/20/2009 02:30 PM 3,854 Grill.params
05/20/2009 10:50 AM <DIR> parameters
05/20/2009 02:39 PM 0 sequest.log
4 File(s) 3,350,044,429 bytes
5 Dir(s) 355,139,117,056 bytes free
C:\Inetpub\wwwroot\ISB\data>
Here comes the output:
-------------------------------------------------
# Commands for session FXXLDZB80 on Wed May 20 14:30:44 2009
# BEGIN COMMAND BLOCK
###### BEGIN Command Execution ######
[Wed May 20 14:30:44 2009] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/
data; runsearch -pc:/Inetpub/wwwroot/ISB/data/Grill.params -P15
BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML.gz
OUTPUT:
RUNSEARCH
Written by J.Eng (c) 2000
MzXML2Search -dta -P15
BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML.gz
MzXML2Search - SEQUEST DTA format
Reading BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML.gz
Getting the index offset
Reading the index
scan: 1 000%
2 000%
3 000%
...
26903 099%
26904 100%
Done.
chmod g+w BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML; cp c:/
Inetpub/wwwroot/ISB/data/Grill.params
BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML
C:\Inetpub\tpp-bin\chmod.exe:
BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML: No such file or
directory
command "C:\Inetpub\tpp-bin\chmod.exe g+w
BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML" failed: Operation not
permitted
cd BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML; find . -maxdepth 1 -
depth -name "BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML*.dta" -
print | xargs --max-args=50 c:/xcalibur/system/programs/
bioworksbrowser/sequest.exe -Pc:/Inetpub/wwwroot/ISB/data/Grill.params
could not chdir to BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML,
error 22 "Invalid argument"
command "C:\Inetpub\tpp-bin\find.exe . -maxdepth 1 -depth -name
"BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML*.dta" -print | xargs --
max-args=50 c:/xcalibur/system/programs/bioworksbrowser/sequest.exe -
Pc:/Inetpub/wwwroot/ISB/data/Grill.params" failed: Unknown error
command "cd BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML; find . -
maxdepth 1 -depth -name
"BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML*.dta" -print | xargs --
max-args=50 c:/xcalibur/system/programs/bioworksbrowser/sequest.exe -
Pc:/Inetpub/wwwroot/ISB/data/Grill.params" failed with exit code 123
Out2XML BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML 1
command "C:\Inetpub\tpp-bin\Out2XML.exe
BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML 1" failed: Unknown
error
command "Out2XML BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML 1"
failed with exit code -1073741819
could not chdir to BN_Grill1_IMACFTTiO2Eluat_1zu5_5h_240409.mzXML ,
error 22 "Invalid argument"
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