PeptideProphet
8 views
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marpello
Mar 26, 2008, 10:56:50 AM3/26/08
to spctools-discuss
Hi,
this is my output:
/usr/local/apps/tpp/bin/xinteract (TPP v3.4 SQUALL rev.0, Build
200802220951)
running: "/usr/local/apps/tpp/bin/InteractParser 'interact.xml' '/usr/
local/apps/tpp/data/002.pepXML'"
file 1: /usr/local/apps/tpp/data/002.pepXML
processed altogether 756 results
results written to file /home/marco/interact.shtml
command completed in 2 sec
running: "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.xml'
MINPROB=0"
(MASCOT) (minprob 0)
results for charge 1: 0 id tot and 0 adj scores
results for charge 2: 1 id tot and 0 adj scores
results for charge 3: 7 id tot and 0 adj scores
results for charge 4: 5 id tot and 0 adj scores
results for charge 5: 0 id tot and 0 adj scores
init with MASCOT Trypsin
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 4
couldnt find 3
couldnt find 3
(....)
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
PeptideProphet v3.0 April 1, 2004 (TPP v3.4 SQUALL rev.0, Build
200802220951) AKeller@ISB
read in 0 1+, 0 2+, 0 3+, 0 4+, and 0 5+ spectra
read in no data
command "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.xml'
MINPROB=0" exited with non-zero exit code: 256
QUIT - the job is incomplete
Any idea?
I need to use Qualscore...but before I must run Xinteract!
Marco
this is my output:
/usr/local/apps/tpp/bin/xinteract (TPP v3.4 SQUALL rev.0, Build
200802220951)
running: "/usr/local/apps/tpp/bin/InteractParser 'interact.xml' '/usr/
local/apps/tpp/data/002.pepXML'"
file 1: /usr/local/apps/tpp/data/002.pepXML
processed altogether 756 results
results written to file /home/marco/interact.shtml
command completed in 2 sec
running: "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.xml'
MINPROB=0"
(MASCOT) (minprob 0)
results for charge 1: 0 id tot and 0 adj scores
results for charge 2: 1 id tot and 0 adj scores
results for charge 3: 7 id tot and 0 adj scores
results for charge 4: 5 id tot and 0 adj scores
results for charge 5: 0 id tot and 0 adj scores
init with MASCOT Trypsin
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 4
couldnt find 3
couldnt find 3
(....)
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
PeptideProphet v3.0 April 1, 2004 (TPP v3.4 SQUALL rev.0, Build
200802220951) AKeller@ISB
read in 0 1+, 0 2+, 0 3+, 0 4+, and 0 5+ spectra
read in no data
command "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.xml'
MINPROB=0" exited with non-zero exit code: 256
QUIT - the job is incomplete
Any idea?
I need to use Qualscore...but before I must run Xinteract!
Marco
Joshua Tasman
Mar 26, 2008, 2:02:05 PM3/26/08
to spctools...@googlegroups.com
Hi Marco,
I recommend installing the latest release (3.5.1) and trying again, as you're using 3.4.0. Please let us know if this helps.
Josh
marpello
Mar 27, 2008, 1:09:56 PM3/27/08
to spctools-discuss
Hi Josh,
I installed the latest release but nothing change!
Other suggestions?
Marco
I installed the latest release but nothing change!
Other suggestions?
Marco
Joshua Tasman
Mar 27, 2008, 1:34:06 PM3/27/08
to spctools...@googlegroups.com
Can you please copy and paste the output with the latest version, just to verify that the output is exactly the same?
-Josh
marpello
Mar 28, 2008, 10:38:40 AM3/28/08
to spctools-discuss
marco@Biochimica2:~$ /usr/local/apps/tppbin/xinteract /usr/local/apps/
tpp/data/002.pepXML
/usr/local/apps/tppbin/xinteract (TPP v3.5 SQUALL rev.1, Build
200803271740 (linux))
running: "/usr/local/apps/tppbin/InteractParser 'interact.pep.xml' '/
command completed in 3 sec
running: "/usr/local/apps/tppbin/PeptideProphetParser
'interact.pep.xml'"
(MASCOT)
200803271740 (linux)) AKeller@ISB
'interact.pep.xml'" exited with non-zero exit code: 256
tpp/data/002.pepXML
/usr/local/apps/tppbin/xinteract (TPP v3.5 SQUALL rev.1, Build
200803271740 (linux))
running: "/usr/local/apps/tppbin/InteractParser 'interact.pep.xml' '/
usr/local/apps/tpp/data/002.pepXML'"
file 1: /usr/local/apps/tpp/data/002.pepXML
processed altogether 756 results
results written to file /home/marco/interact.pep.shtml
file 1: /usr/local/apps/tpp/data/002.pepXML
processed altogether 756 results
command completed in 3 sec
running: "/usr/local/apps/tppbin/PeptideProphetParser
'interact.pep.xml'"
(MASCOT)
results for charge 1: 0 id tot and 0 adj scores
results for charge 2: 1 id tot and 0 adj scores
results for charge 3: 7 id tot and 0 adj scores
results for charge 4: 5 id tot and 0 adj scores
results for charge 5: 0 id tot and 0 adj scores
init with MASCOT Trypsin
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 4
couldnt find 3
couldnt find 3
results for charge 2: 1 id tot and 0 adj scores
results for charge 3: 7 id tot and 0 adj scores
results for charge 4: 5 id tot and 0 adj scores
results for charge 5: 0 id tot and 0 adj scores
init with MASCOT Trypsin
couldnt find 3
couldnt find 3
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couldnt find 4
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couldnt find 3
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
PeptideProphet v3.0 April 1, 2004 (TPP v3.5 SQUALL rev.1, Build
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
couldnt find 3
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
200803271740 (linux)) AKeller@ISB
read in 0 1+, 0 2+, 0 3+, 0 4+, and 0 5+ spectra
read in no data
command "/usr/local/apps/tppbin/PeptideProphetParser
read in no data
'interact.pep.xml'" exited with non-zero exit code: 256
Melody Lam
Nov 19, 2009, 5:46:18 AM11/19/09
to marpello, spctools...@googlegroups.com
Dear all,
Sorry for digging up this old post. But I have encountered the same
problem again.
I am using the command line version of TPP(4.3.0) in WinXP (SP3),
using the pepXML files exported from Mascot.
There are unknown error of "couldnt find 3" when I am using the
PeptideProphet. [ Output attached below ]
Thanks in advance for your advance and options on this.
Regards,
Melody Lam
---------------------------------------------------------------------------------------------
Output from xinteract
----------------------------------------------------------------------------------
xinteract (TPP v4.3 JETSTREAM rev 0, Build 200908071234 (MinGW))
running: "C:/Inetpub/tpp-bin/InteractParser "C:/Inetpub/wwwroot/tmp/
a01840/ISB/data/probidoutput/dat/ipi/interact.pep.xml" "ipi1.2-
dF006117.xml" "ipi1.2_all_F006117.xml" -L"7""
file 1: ipi1.2-dF006117.xml
file 2: ipi1.2_all_F006117.xml
processed altogether 9099 results
results written to file c:/Inetpub/wwwroot/tmp/a01840/ISB/data/
probidoutput/dat/ipi/interact.pep.xml
direct your browser to http://localhost/interact.pep.shtml
command completed in 64 sec
running: "C:/Inetpub/tpp-bin/PeptideProphetParser "C:/Inetpub/wwwroot/
tmp/a01840
/ISB/data/probidoutput/dat/ipi/interact.pep.xml" MINPROB=0.05 ACCMASS
MALDI IGNO
RECHG=2 IGNORECHG=3 IGNORECHG=4 IGNORECHG=5 IGNORECHG=6 IGNORECHG=7"
using Accurate Mass Bins
maldi mode
Ignoring charge 2+ spectra.
Ignoring charge 3+ spectra.
Ignoring charge 4+ spectra.
Ignoring charge 5+ spectra.
Ignoring charge 6+ spectra.
Ignoring charge 7+ spectra.
(MASCOT)
results for charge 1: 87 id tot and 0 adj scores
adding Accurate Mass mixture distr
results for charge 2: 0 id tot and 0 adj scores
results for charge 3: 0 id tot and 0 adj scores
results for charge 4: 0 id tot and 0 adj scores
results for charge 7: 0 id tot and 0 adj scores
(MinGW)) AKeller@
ISB
read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
read in no data
command "C:/Inetpub/tpp-bin/PeptideProphetParser "C:/Inetpub/wwwroot/
tmp/a01840/
ISB/data/probidoutput/dat/ipi/interact.pep.xml" MINPROB=0.05 ACCMASS
MALDI IGNOR
ECHG=2 IGNORECHG=3 IGNORECHG=4 IGNORECHG=5 IGNORECHG=6 IGNORECHG=7"
failed: Oper
ation not permitted
command "C:/Inetpub/tpp-bin/PeptideProphetParser "C:/Inetpub/wwwroot/
tmp/a01840/
ISB/data/probidoutput/dat/ipi/interact.pep.xml" MINPROB=0.05 ACCMASS
MALDI IGNOR
ECHG=2 IGNORECHG=3 IGNORECHG=4 IGNORECHG=5 IGNORECHG=6 IGNORECHG=7"
exited with
non-zero exit code: 1
> couldnt find 3 ...
>
> read more »
Sorry for digging up this old post. But I have encountered the same
problem again.
I am using the command line version of TPP(4.3.0) in WinXP (SP3),
using the pepXML files exported from Mascot.
There are unknown error of "couldnt find 3" when I am using the
PeptideProphet. [ Output attached below ]
Thanks in advance for your advance and options on this.
Regards,
Melody Lam
---------------------------------------------------------------------------------------------
Output from xinteract
----------------------------------------------------------------------------------
xinteract (TPP v4.3 JETSTREAM rev 0, Build 200908071234 (MinGW))
running: "C:/Inetpub/tpp-bin/InteractParser "C:/Inetpub/wwwroot/tmp/
a01840/ISB/data/probidoutput/dat/ipi/interact.pep.xml" "ipi1.2-
dF006117.xml" "ipi1.2_all_F006117.xml" -L"7""
file 1: ipi1.2-dF006117.xml
file 2: ipi1.2_all_F006117.xml
processed altogether 9099 results
results written to file c:/Inetpub/wwwroot/tmp/a01840/ISB/data/
probidoutput/dat/ipi/interact.pep.xml
direct your browser to http://localhost/interact.pep.shtml
command completed in 64 sec
running: "C:/Inetpub/tpp-bin/PeptideProphetParser "C:/Inetpub/wwwroot/
tmp/a01840
/ISB/data/probidoutput/dat/ipi/interact.pep.xml" MINPROB=0.05 ACCMASS
MALDI IGNO
RECHG=2 IGNORECHG=3 IGNORECHG=4 IGNORECHG=5 IGNORECHG=6 IGNORECHG=7"
using Accurate Mass Bins
maldi mode
Ignoring charge 2+ spectra.
Ignoring charge 3+ spectra.
Ignoring charge 4+ spectra.
Ignoring charge 5+ spectra.
Ignoring charge 6+ spectra.
Ignoring charge 7+ spectra.
(MASCOT)
results for charge 1: 87 id tot and 0 adj scores
adding Accurate Mass mixture distr
results for charge 2: 0 id tot and 0 adj scores
results for charge 3: 0 id tot and 0 adj scores
results for charge 4: 0 id tot and 0 adj scores
results for charge 5: 0 id tot and 0 adj scores
results for charge 6: 0 id tot and 0 adj scores
results for charge 7: 0 id tot and 0 adj scores
init with MASCOT Trypsin
couldnt find 3
couldnt find 3
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MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
UNKNOWN,
Analyzer: UNKNOWN, Detector: UNKNOWN
PeptideProphet (TPP v4.3 JETSTREAM rev 0, Build 200908071234
UNKNOWN,
Analyzer: UNKNOWN, Detector: UNKNOWN
(MinGW)) AKeller@
ISB
read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
read in no data
command "C:/Inetpub/tpp-bin/PeptideProphetParser "C:/Inetpub/wwwroot/
tmp/a01840/
ISB/data/probidoutput/dat/ipi/interact.pep.xml" MINPROB=0.05 ACCMASS
MALDI IGNOR
ECHG=2 IGNORECHG=3 IGNORECHG=4 IGNORECHG=5 IGNORECHG=6 IGNORECHG=7"
failed: Oper
ation not permitted
command "C:/Inetpub/tpp-bin/PeptideProphetParser "C:/Inetpub/wwwroot/
tmp/a01840/
ISB/data/probidoutput/dat/ipi/interact.pep.xml" MINPROB=0.05 ACCMASS
MALDI IGNOR
ECHG=2 IGNORECHG=3 IGNORECHG=4 IGNORECHG=5 IGNORECHG=6 IGNORECHG=7"
exited with
non-zero exit code: 1
>
> read more »
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