non-zero exit code: 32512

[CH]

I'm trying to run ProteinProphet and ASAPRatio

Error with trying to run ProteinProphet:
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the
original Perl by A. Keller (TPP v3.0 SQUALL rev.0, Build 200703291728)
(xml input) (using degen pep info)
error opening /cygdrive/c/Inetpub/wwwroot/ISB/data/tpp_newversiontest/
3_0_0/Heavy/cn109_silac_c_jl_rh_01.xml /cygdrive/c/Inetpub/wwwroot/ISB/
data/tpp_newversiontest/3_0_0/Light/cn109_silac_c_jl_rh_01.xml
Error: No database referenced by /cygdrive/c/Inetpub/wwwroot/ISB/data/
tpp_newversiontest/3_0_0/Heavy/cn109_silac_c_jl_rh_01.xml /cygdrive/c/
Inetpub/wwwroot/ISB/data/tpp_newversiontest/3_0_0/Light/
cn109_silac_c_jl_rh_01.xml

This is the error with ASAPRatio:
command "/usr/bin/ProteinProphet 'quant_interact.xml' 'quant_interact-
prot.xml' XML" exited with non-zero exit code: 32512
QUIT - the job is incomplete

Help on how to troubleshoot or fix this please. Thanks in advance.

[Brian Pratt]

What does your xinteract command line and output log look like?

- Brian

[David Shteynberg]

There have been some recent commit in CVS to fix ProteinProphet memory
issues under certain condition. We have not released a package that
contains these fixes yet. However, you can try to replace your version
of ProteinProphet.exe in /cygdrive/c/cygwin/bin with the recompiled
executable which I posted at the following link:
http://tools.proteomecenter.org/software/ProteinProphet.exe

Let us know if the new binary works for you.

-David

[CH]

I apologize for the delay in getting back.

I replaced ProteinProphet with the version you provided.

Here is the error:
cd /cygdrive/c/Inetpub/wwwroot/ISB/data/test_cn/adenokfive/
H8PM_111805; /usr/bin/xinteract -Ninteract.xml -p0.05 -x20 -Op /
cygdrive/c/Inetpub/wwwroot/ISB/data/test_cn/adenokfive/H8PM_111805/
Light/1118H8pm_01.xml
--------------------------------------------------------------------------------

/usr/bin/xinteract (TPP v3.0 SQUALL rev.0, Build 200703291728)

running: "/usr/bin/InteractParser 'interact.xml' '/cygdrive/c/Inetpub/
wwwroot/ISB/data/test_cn/adenokfive/H8PM_111805/Light/
1118H8pm_01.xml'"
file 1: /cygdrive/c/Inetpub/wwwroot/ISB/data/test_cn/adenokfive/
H8PM_111805/Light/1118H8pm_01.xml
processed altogether 4074 results

results written to file c:\Inetpub\wwwroot\ISB\data\test_cn\adenokfive
\H8PM_111805\interact.xml

direct your browser to http://localhost:1441/ISB/data/test_cn/adenokfive/H8PM_111805/interact.shtml

command completed in 15 sec

running: "/usr/bin/PeptideProphetParser 'interact.xml' MINPROB=0.05
EXTRAITRS=20"
(SEQUEST)
init with SEQUEST trypsin
MS Instrument info: Manufacturer: ThermoFinnigan, Model: LCQ Deca XP,
Ionization: ESI, Analyzer: Ion Trap, Detector: EMT

PeptideProphet v3.0 April 1, 2004 (TPP v3.0 SQUALL rev.0, Build
200703291728) AKeller@ISB
read in 29 1+, 2068 2+, 1977 3+, 0 4+, and 0 5+ spectra
model complete after 25 iterations
command completed in 13 sec

running: "/usr/bin/DatabaseParser 'interact.xml'"
command completed in 0 sec

running: "/usr/bin/RefreshParser 'interact.xml' 'C:\Xcalibur\database
\ipi.HUMAN.v3.23.fasta'"
- Building Commentz-Walter keyword tree... - Searching the tree...
- Linking duplicate entries... - Printing results...

command completed in 20 sec

running: "/usr/bin/ProteinProphet 'interact.xml' 'interact-prot.xml'
XML"

ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the

original Perl by A. Keller (TPP v3.0 SQUALL rev.0, Build 200703131613)

(xml input) (using degen pep info)

. . . reading in /cygdrive/c/Inetpub/wwwroot/ISB/data/test_cn/
adenokfive/H8PM_111805/interact.xml. . .
. . . read in 0 1+, 158 2+, and 237 3+ spectra with min prob 0.05
sh: c:/inetpub/wwwroot../tpp-bin/protxml2html.pl: No such file or
directory
c:/inetpub/wwwroot../tpp-bin/protxml2html.pl -file "/cygdrive/c/
Inetpub/wwwroot/ISB/data/test_cn/adenokfive/H8PM_111805/interact-
prot.xml" 335 failed with code 32512

command "/usr/bin/ProteinProphet 'interact.xml' 'interact-prot.xml'

XML" exited with non-zero exit code: 32512
QUIT - the job is incomplete

Any help would be appreciated!

Thank you!

On Apr 6, 4:57 pm, "David Shteynberg" <dshte...@systemsbiology.org>
wrote:

> Help on how to troubleshoot or fix this please. Thanks in advance.- Hide quoted text -
>
> - Show quoted text -

[Joshua Tasman]

The problem you're seeing now has nothing to do with the ProteinProphet
memory issue. It looks like you're missing a file that ProteinProphet
relies on for conversion of protXML to html, perhaps due to an
incomplete installation?

> sh: c:/inetpub/wwwroot../tpp-bin/protxml2html.pl: No such file or
> directory

Perhaps you should save the newer version of ProteinProphet, reinstall
the tools, and copy over the new ProteinProphet program again.

Josh

[CH]

I did what was suggested. By reinstalling do you mean downloading and
running setup.exe again? If so, I did that and I have the same
problem with the same error.

Would it help if I told you we had version 2.9.2 installed before
updating with version 3.0.0 without installing any of the versions in
between 2.9.2 and 3.0.0?

[Joshua Tasman]

Yes, that's correct, I did mean running setup.exe again. (You actually
don't have to re-download it, as it gets the actually installation files
from our server.) Can you clarify which error you're referring to? Do
you mean the missing file I'd mentioned today, or a ProteinProphet
error? In the message you'd copied most recently, I see

Error: No database referenced by
/cygdrive/c/Inetpub/wwwroot/ISB/data/tpp_newversiontest/3_0_0/Heavy/cn109_silac_c_jl_rh_01.xml
/cygdrive/c/Inetpub/wwwroot/ISB/data/tpp_newversiontest/3_0_0/Light/cn109_silac_c_jl_rh_01.xml

Which sounds like your database is not accessable or not specified
correctly.

You shouldn't need to install any intermediate versions, although it is
possible that you've helped to reveal a bug that somehow doesn't come up
unless you skip those installations. We'll keep trying to figure it out.

Josh

[CH]

Hmm. I didn't notice the different errors. I tried running Protein
Prophet and ASAPRatio again on the exact files that produced the
database error and I haven't seen it again. I do see the
protxml2html.pl errors. I've entered the log files below. When
running setup.exe again I get a window that pops up and say Nothing
needed to be installed.

With running Protein Prophet only I get:

cd /cygdrive/c/Inetpub/wwwroot/ISB/data/test_cn/adenokfive/
H8PM_111805; /usr/bin/xinteract -Ninteract.xml -p0.05 -x20 -Op /
cygdrive/c/Inetpub/wwwroot/ISB/data/test_cn/adenokfive/H8PM_111805/
Light/1118H8pm_01.xml
--------------------------------------------------------------------------------

/usr/bin/xinteract (TPP v3.0 SQUALL rev.0, Build 200703291728)

running: "/usr/bin/InteractParser 'interact.xml' '/cygdrive/c/Inetpub/
wwwroot/ISB/data/test_cn/adenokfive/H8PM_111805/Light/
1118H8pm_01.xml'"
file 1: /cygdrive/c/Inetpub/wwwroot/ISB/data/test_cn/adenokfive/
H8PM_111805/Light/1118H8pm_01.xml
processed altogether 4074 results

results written to file c:\Inetpub\wwwroot\ISB\data\test_cn\adenokfive
\H8PM_111805\interact.xml

direct your browser to http://localhost:1441/ISB/data/test_cn/adenokfive/H8PM_111805/interact.shtml

command completed in 14 sec

running: "/usr/bin/PeptideProphetParser 'interact.xml' MINPROB=0.05
EXTRAITRS=20"
(SEQUEST)
init with SEQUEST trypsin
MS Instrument info: Manufacturer: ThermoFinnigan, Model: LCQ Deca XP,
Ionization: ESI, Analyzer: Ion Trap, Detector: EMT

PeptideProphet v3.0 April 1, 2004 (TPP v3.0 SQUALL rev.0, Build
200703291728) AKeller@ISB
read in 29 1+, 2068 2+, 1977 3+, 0 4+, and 0 5+ spectra
model complete after 25 iterations

command completed in 12 sec

running: "/usr/bin/DatabaseParser 'interact.xml'"
command completed in 0 sec

running: "/usr/bin/RefreshParser 'interact.xml' 'C:\Xcalibur\database
\ipi.HUMAN.v3.23.fasta'"
- Building Commentz-Walter keyword tree... - Searching the tree...
- Linking duplicate entries... - Printing results...

command completed in 19 sec

running: "/usr/bin/ProteinProphet 'interact.xml' 'interact-prot.xml'
XML"

ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the

original Perl by A. Keller (TPP v3.0 SQUALL rev.0, Build 200703131613)

(xml input) (using degen pep info)

. . . reading in /cygdrive/c/Inetpub/wwwroot/ISB/data/test_cn/
adenokfive/H8PM_111805/interact.xml. . .
. . . read in 0 1+, 158 2+, and 237 3+ spectra with min prob 0.05

sh: c:/Inetpub/wwwroot../tpp-bin/protxml2html.pl: No such file or
directory
c:/Inetpub/wwwroot../tpp-bin/protxml2html.pl -file "/cygdrive/c/

Inetpub/wwwroot/ISB/data/test_cn/adenokfive/H8PM_111805/interact-
prot.xml" 335 failed with code 32512

command "/usr/bin/ProteinProphet 'interact.xml' 'interact-prot.xml'

XML" exited with non-zero exit code: 32512
QUIT - the job is incomplete

Command FAILED

This is what I see when running ProteinProphet with ASAPRatio.
cd /cygdrive/c/Inetpub/wwwroot/ISB/data/0524K5PM; /usr/bin/xinteract -
Ninteract.xml -p0.05 -x20 -Op -A-lKL-r0.5-S-mK128.1741L113.1594 /
cygdrive/c/Inetpub/wwwroot/ISB/data/0524K5PM/Heavy/0524pm_01.xml /
cygdrive/c/Inetpub/wwwroot/ISB/data/0524K5PM/Light/0524pm_01.xml
--------------------------------------------------------------------------------

/usr/bin/xinteract (TPP v3.0 SQUALL rev.0, Build 200703291728)

running: "/usr/bin/InteractParser 'interact.xml' '/cygdrive/c/Inetpub/
wwwroot/ISB/data/0524K5PM/Heavy/0524pm_01.xml' '/cygdrive/c/Inetpub/
wwwroot/ISB/data/0524K5PM/Light/0524pm_01.xml'"
file 1: /cygdrive/c/Inetpub/wwwroot/ISB/data/0524K5PM/Heavy/
0524pm_01.xml
file 2: /cygdrive/c/Inetpub/wwwroot/ISB/data/0524K5PM/Light/
0524pm_01.xml
processed altogether 1830 results

results written to file c:\Inetpub\wwwroot\ISB\data\0524K5PM
\interact.xml

direct your browser to http://localhost:1441/ISB/data/0524K5PM/interact.shtml

command completed in 8 sec

running: "/usr/bin/PeptideProphetParser 'interact.xml' MINPROB=0.05
EXTRAITRS=20"
(SEQUEST)
init with SEQUEST trypsin

--------------------------------------------------------------------------------
...skipping 317 lines of output...
--------------------------------------------------------------------------------

running: "/usr/bin/DatabaseParser 'interact.xml'"
command completed in 0 sec

running: "/usr/bin/RefreshParser 'interact.xml' 'C:\Xcalibur\database

\66uniprot_sprot_human_eric.fasta'"

- Building Commentz-Walter keyword tree... - Searching the tree...
- Linking duplicate entries... - Printing results...

command completed in 9 sec

running: "/usr/bin/ProteinProphet 'interact.xml' 'interact-prot.xml'
XML"

ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the

original Perl by A. Keller (TPP v3.0 SQUALL rev.0, Build 200703131613)

(xml input) (using degen pep info)

. . . reading in /cygdrive/c/Inetpub/wwwroot/ISB/data/0524K5PM/
interact.xml. . .
. . . read in 15 1+, 195 2+, and 171 3+ spectra with min prob 0.05
sh: c:/Inetpub/wwwroot../tpp-bin/protxml2html.pl: No such file or
directory
c:/Inetpub/wwwroot../tpp-bin/protxml2html.pl -file "/cygdrive/c/
Inetpub/wwwroot/ISB/data/0524K5PM/interact-prot.xml" 263 failed with
code 32512

command "/usr/bin/ProteinProphet 'interact.xml' 'interact-prot.xml'

XML" exited with non-zero exit code: 32512
QUIT - the job is incomplete

Command FAILED

Thanks again for your help.

[Joshua Tasman]

Thanks for explaining and posting the detailed logs. I still believe
this is a corrupted installation. Rereun the cygwin setup program, and
when you get to the "Select Packages" pane, expand "Base", find
"ISB-MS-Tools" (should be the first entry), and click "Keep" until it
cycles to "Reinstall", then proceed as usual.

Josh

[CH]

It looks like it worked (yay!). Thanks for the detailed directions
you gave me and patience for someone who isn't very computer-savvy.

> > direct your browser tohttp://localhost:1441/ISB/data/test_cn/adenokfive/H8PM_111805/interac...

> > direct your browser tohttp://localhost:1441/ISB/data/0524K5PM/interact.shtml