I have installed TPP v4.2 on windows XP. I have created the mzXML
datafiles from my Sequest search. Now I'm making the corresponding
pepXML files. I see that the first file is being created, it seems
that is finished but I see the following warming message at the end of
the “Output so far” field:
warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
test.mzXML" for reading MS instrument info and scan times.
And the command status window indicates that the command is still
running. Is it? I do not see the file increasing in size. I can open
the pepxml file, although IE indicates that there is an error on page.
It seems to me that the program is stuck and is not progressing to
next task: the creation of the next pepXML file. Solutions?
The mzXML files should correspond to the same raw file input used for
your Sequest search. For example if starting from a Thermo .raw file,
you'd convert that mzXML, search that, and then convert the search
results to pepXML.
Note that the pepXML files refer to specific file locations, so if
you've moved your mzXML file since it was first created, the TPP might
be confused.
Hope this helps and let us know how it goes,
Natalie
> I have installed TPP v4.2 on windows XP. I have created the mzXML
> datafiles from my Sequest search. Now I'm making the corresponding
> pepXML files. I see that the first file is being created, it seems
> that is finished but I see the following warming message at the end of
> the “Output so far” field:
> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
> test.mzXML" for reading MS instrument info and scan times.
> And the command status window indicates that the command is still
> running. Is it? I do not see the file increasing in size. I can open
> the pepxml file, although IE indicates that there is an error on page.
> It seems to me that the program is stuck and is not progressing to
> next task: the creation of the next pepXML file. Solutions?
That warning about not being able to open the mzXML file is not indicative of the underlying problem. It is truly just a warning and the analysis process is capable of finishing correctly even if the corresponding mzXML file is missing.
The important question that's not clear from your description below is how did you run the Sequest search? Did you run it separately via Bioworks or did you run the search through the TPP? Although helpful but not required, it doesn't seem like you did the latter. Do you have a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has the Sequest .out files in it?
Antonio wrote:
> I have installed TPP v4.2 on windows XP. I have created the mzXML
> datafiles from my Sequest search. Now I'm making the corresponding
> pepXML files. I see that the first file is being created, it seems
> that is finished but I see the following warming message at the end of
> the “Output so far” field:
> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
> test.mzXML" for reading MS instrument info and scan times.
> And the command status window indicates that the command is still
> running. Is it? I do not see the file increasing in size. I can open
> the pepxml file, although IE indicates that there is an error on page.
> It seems to me that the program is stuck and is not progressing to
> next task: the creation of the next pepXML file. Solutions?
I run Sequest from Bioworks on our computer cluster, and then transfer
the files to the local machine running TPP, so yeas I had the c:/
Inetpub/wwwroot/ISB/data/AAS/test/
With the out-and dta- files in it.
I have attempted to run Sequest from TPP and I had the same problem;
the dta and out files are created, but the command indicates that is
still running. The problem occurs whether I send a few files or a
single one. But I have more than one file on the queue, the command
will not proceed to the next file. I can run Sequest from Bioworks on
the local machine without any problems.
On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> That warning about not being able to open the mzXML file is not
> indicative of the underlying problem. It is truly just a warning and
> the analysis process is capable of finishing correctly even if the
> corresponding mzXML file is missing.
> The important question that's not clear from your description below is
> how did you run the Sequest search? Did you run it separately via
> Bioworks or did you run the search through the TPP? Although helpful
> but not required, it doesn't seem like you did the latter. Do you have
> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has the
> Sequest .out files in it?
> - Jimmy
> Antonio wrote:
> > I have installed TPP v4.2 on windows XP. I have created the mzXML
> > datafiles from my Sequest search. Now I'm making the corresponding
> > pepXML files. I see that the first file is being created, it seems
> > that is finished but I see the following warming message at the end of
> > the “Output so far” field:
> > warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
> > test.mzXML" for reading MS instrument info and scan times.
> > And the command status window indicates that the command is still
> > running. Is it? I do not see the file increasing in size. I can open
> > the pepxml file, although IE indicates that there is an error on page.
> > It seems to me that the program is stuck and is not progressing to
> > next task: the creation of the next pepXML file. Solutions?
cd c:/Inetpub/wwwroot/ISB/data/AAS/
Out2XML basename 1
This should create basename.pep.xml in the AAS directory. This simple exercise is just to confirm that it runs through correctly and the process finishes. The next thing to try is to repeat the above data structure but try the pepXML conversion in the GUI. Hopefully this isolates whether you're experiencing a pepXML conversion problem or a GUI problem.
> I run Sequest from Bioworks on our computer cluster, and then transfer
> the files to the local machine running TPP, so yeas I had the c:/
> Inetpub/wwwroot/ISB/data/AAS/test/
> With the out-and dta- files in it.
> I have attempted to run Sequest from TPP and I had the same problem;
> the dta and out files are created, but the command indicates that is
> still running. The problem occurs whether I send a few files or a
> single one. But I have more than one file on the queue, the command
> will not proceed to the next file. I can run Sequest from Bioworks on
> the local machine without any problems.
> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>> Antonio,
>> That warning about not being able to open the mzXML file is not
>> indicative of the underlying problem. It is truly just a warning and
>> the analysis process is capable of finishing correctly even if the
>> corresponding mzXML file is missing.
>> The important question that's not clear from your description below is
>> how did you run the Sequest search? Did you run it separately via
>> Bioworks or did you run the search through the TPP? Although helpful
>> but not required, it doesn't seem like you did the latter. Do you have
>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has the
>> Sequest .out files in it?
>> - Jimmy
>> Antonio wrote:
>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
>>> datafiles from my Sequest search. Now I'm making the corresponding
>>> pepXML files. I see that the first file is being created, it seems
>>> that is finished but I see the following warming message at the end of
>>> the “Output so far” field:
>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
>>> test.mzXML" for reading MS instrument info and scan times.
>>> And the command status window indicates that the command is still
>>> running. Is it? I do not see the file increasing in size. I can open
>>> the pepxml file, although IE indicates that there is an error on page.
>>> It seems to me that the program is stuck and is not progressing to
>>> next task: the creation of the next pepXML file. Solutions?
>>> Thanks,
>>> Antonio- Hide quoted text -
>> - Show quoted text -
OK, done it. No problem, the command were successfull, all finished,
th eTPP window indicated that the command was sucessfull and is
finished. i can open the basename.pep on TPP and all seens OK.
What next?
Antonio
On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> cd c:/Inetpub/wwwroot/ISB/data/AAS/
> Out2XML basename 1
> This should create basename.pep.xml in the AAS directory. This simple
> exercise is just to confirm that it runs through correctly and the
> process finishes. The next thing to try is to repeat the above data
> structure but try the pepXML conversion in the GUI. Hopefully this
> isolates whether you're experiencing a pepXML conversion problem or a
> GUI problem.
> - Jimmy
> Antonio wrote:
> > Hi Jimmy,
> > I run Sequest from Bioworks on our computer cluster, and then transfer
> > the files to the local machine running TPP, so yeas I had the c:/
> > Inetpub/wwwroot/ISB/data/AAS/test/
> > With the out-and dta- files in it.
> > I have attempted to run Sequest from TPP and I had the same problem;
> > the dta and out files are created, but the command indicates that is
> > still running. The problem occurs whether I send a few files or a
> > single one. But I have more than one file on the queue, the command
> > will not proceed to the next file. I can run Sequest from Bioworks on
> > the local machine without any problems.
> > On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> >> Antonio,
> >> That warning about not being able to open the mzXML file is not
> >> indicative of the underlying problem. It is truly just a warning and
> >> the analysis process is capable of finishing correctly even if the
> >> corresponding mzXML file is missing.
> >> The important question that's not clear from your description below is
> >> how did you run the Sequest search? Did you run it separately via
> >> Bioworks or did you run the search through the TPP? Although helpful
> >> but not required, it doesn't seem like you did the latter. Do you have
> >> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has the
> >> Sequest .out files in it?
> >> - Jimmy
> >> Antonio wrote:
> >>> I have installed TPP v4.2 on windows XP. I have created the mzXML
> >>> datafiles from my Sequest search. Now I'm making the corresponding
> >>> pepXML files. I see that the first file is being created, it seems
> >>> that is finished but I see the following warming message at the end of
> >>> the “Output so far” field:
> >>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
> >>> test.mzXML" for reading MS instrument info and scan times.
> >>> And the command status window indicates that the command is still
> >>> running. Is it? I do not see the file increasing in size. I can open
> >>> the pepxml file, although IE indicates that there is an error on page.
> >>> It seems to me that the program is stuck and is not progressing to
> >>> next task: the creation of the next pepXML file. Solutions?
> >>> Thanks,
> >>> Antonio- Hide quoted text -
> >> - Show quoted text -- Hide quoted text -
I guess the next step is to repeat the pepXML conversion from the GUI and see if the GUI reports that the command completed successfully. If it does, organize a couple of search directories using the same structure and repeat the pepXML conversion. Still getting stuck or is the processes reported to be completed?
If if looks like the first pepXML file is generated/completed but the interface thinks the command is still running, I'm going to need Luis to chime in on what to look for as I've exhausted the bits I have knowledge of. So let us know what happens when you try the above.
> OK, done it. No problem, the command were successfull, all finished,
> th eTPP window indicated that the command was sucessfull and is
> finished. i can open the basename.pep on TPP and all seens OK.
> What next?
> Antonio
> On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>> Antonio,
>> Can you try this. Replace "basename" with one of your RAW/mzXML file
>> base name (i.e. <basename>.mzXML)
>> cd c:/Inetpub/wwwroot/ISB/data/AAS/
>> Out2XML basename 1
>> This should create basename.pep.xml in the AAS directory. This simple
>> exercise is just to confirm that it runs through correctly and the
>> process finishes. The next thing to try is to repeat the above data
>> structure but try the pepXML conversion in the GUI. Hopefully this
>> isolates whether you're experiencing a pepXML conversion problem or a
>> GUI problem.
>> - Jimmy
>> Antonio wrote:
>>> Hi Jimmy,
>>> I run Sequest from Bioworks on our computer cluster, and then transfer
>>> the files to the local machine running TPP, so yeas I had the c:/
>>> Inetpub/wwwroot/ISB/data/AAS/test/
>>> With the out-and dta- files in it.
>>> I have attempted to run Sequest from TPP and I had the same problem;
>>> the dta and out files are created, but the command indicates that is
>>> still running. The problem occurs whether I send a few files or a
>>> single one. But I have more than one file on the queue, the command
>>> will not proceed to the next file. I can run Sequest from Bioworks on
>>> the local machine without any problems.
>>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>> Antonio,
>>>> That warning about not being able to open the mzXML file is not
>>>> indicative of the underlying problem. It is truly just a warning and
>>>> the analysis process is capable of finishing correctly even if the
>>>> corresponding mzXML file is missing.
>>>> The important question that's not clear from your description below is
>>>> how did you run the Sequest search? Did you run it separately via
>>>> Bioworks or did you run the search through the TPP? Although helpful
>>>> but not required, it doesn't seem like you did the latter. Do you have
>>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has the
>>>> Sequest .out files in it?
>>>> - Jimmy
>>>> Antonio wrote:
>>>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
>>>>> datafiles from my Sequest search. Now I'm making the corresponding
>>>>> pepXML files. I see that the first file is being created, it seems
>>>>> that is finished but I see the following warming message at the end of
>>>>> the “Output so far” field:
>>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>> test.mzXML" for reading MS instrument info and scan times.
>>>>> And the command status window indicates that the command is still
>>>>> running. Is it? I do not see the file increasing in size. I can open
>>>>> the pepxml file, although IE indicates that there is an error on page.
>>>>> It seems to me that the program is stuck and is not progressing to
>>>>> next task: the creation of the next pepXML file. Solutions?
>>>>> Thanks,
>>>>> Antonio- Hide quoted text -
>>>> - Show quoted text -- Hide quoted text -
>> - Show quoted text -
> I guess the next step is to repeat the pepXML conversion from the GUI
> and see if the GUI reports that the command completed successfully. If
> it does, organize a couple of search directories using the same
> structure and repeat the pepXML conversion. Still getting stuck or is
> the processes reported to be completed?
> If if looks like the first pepXML file is generated/completed but the
> interface thinks the command is still running, I'm going to need Luis to
> chime in on what to look for as I've exhausted the bits I have knowledge
> of. So let us know what happens when you try the above.
> - Jimmy
> Antonio wrote:
> > Hi Jimmy,
> > OK, done it. No problem, the command were successfull, all finished,
> > th eTPP window indicated that the command was sucessfull and is
> > finished. i can open the basename.pep on TPP and all seens OK.
> > What next?
> > Antonio
> > On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> >> Antonio,
> >> Can you try this. Replace "basename" with one of your RAW/mzXML file
> >> base name (i.e. <basename>.mzXML)
> >> cd c:/Inetpub/wwwroot/ISB/data/AAS/
> >> Out2XML basename 1
> >> This should create basename.pep.xml in the AAS directory. This simple
> >> exercise is just to confirm that it runs through correctly and the
> >> process finishes. The next thing to try is to repeat the above data
> >> structure but try the pepXML conversion in the GUI. Hopefully this
> >> isolates whether you're experiencing a pepXML conversion problem or a
> >> GUI problem.
> >> - Jimmy
> >> Antonio wrote:
> >>> Hi Jimmy,
> >>> I run Sequest from Bioworks on our computer cluster, and then transfer
> >>> the files to the local machine running TPP, so yeas I had the c:/
> >>> Inetpub/wwwroot/ISB/data/AAS/test/
> >>> With the out-and dta- files in it.
> >>> I have attempted to run Sequest from TPP and I had the same problem;
> >>> the dta and out files are created, but the command indicates that is
> >>> still running. The problem occurs whether I send a few files or a
> >>> single one. But I have more than one file on the queue, the command
> >>> will not proceed to the next file. I can run Sequest from Bioworks on
> >>> the local machine without any problems.
> >>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> >>>> Antonio,
> >>>> That warning about not being able to open the mzXML file is not
> >>>> indicative of the underlying problem. It is truly just a warning and
> >>>> the analysis process is capable of finishing correctly even if the
> >>>> corresponding mzXML file is missing.
> >>>> The important question that's not clear from your description below is
> >>>> how did you run the Sequest search? Did you run it separately via
> >>>> Bioworks or did you run the search through the TPP? Although helpful
> >>>> but not required, it doesn't seem like you did the latter. Do you have
> >>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has the
> >>>> Sequest .out files in it?
> >>>> - Jimmy
> >>>> Antonio wrote:
> >>>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
> >>>>> datafiles from my Sequest search. Now I'm making the corresponding
> >>>>> pepXML files. I see that the first file is being created, it seems
> >>>>> that is finished but I see the following warming message at the end of
> >>>>> the “Output so far” field:
> >>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
> >>>>> test.mzXML" for reading MS instrument info and scan times.
> >>>>> And the command status window indicates that the command is still
> >>>>> running. Is it? I do not see the file increasing in size. I can open
> >>>>> the pepxml file, although IE indicates that there is an error on page.
> >>>>> It seems to me that the program is stuck and is not progressing to
> >>>>> next task: the creation of the next pepXML file. Solutions?
> >>>>> Thanks,
> >>>>> Antonio- Hide quoted text -
> >>>> - Show quoted text -- Hide quoted text -
> >> - Show quoted text -- Hide quoted text -
Hi Jimmy,
I have repeated the process from TPP. The command gets stuck either
after sending the Sequest search or creating the pepXML file. I might
have to reinstall pearl and TPP.
Antonio
On Jul 9, 2:41 pm, Antonio <aartig...@kumc.edu> wrote:
> Ok Jimmy,
> Thank you very much for your help.
> I'll repeat the entire process from TPP and I will let you know the
> result.
> Regards,
> Antonio
> On Jul 9, 2:18 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> > I guess the next step is to repeat the pepXML conversion from the GUI
> > and see if the GUI reports that the command completed successfully. If
> > it does, organize a couple of search directories using the same
> > structure and repeat the pepXML conversion. Still getting stuck or is
> > the processes reported to be completed?
> > If if looks like the first pepXML file is generated/completed but the
> > interface thinks the command is still running, I'm going to need Luis to
> > chime in on what to look for as I've exhausted the bits I have knowledge
> > of. So let us know what happens when you try the above.
> > - Jimmy
> > Antonio wrote:
> > > Hi Jimmy,
> > > OK, done it. No problem, the command were successfull, all finished,
> > > th eTPP window indicated that the command was sucessfull and is
> > > finished. i can open the basename.pep on TPP and all seens OK.
> > > What next?
> > > Antonio
> > > On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> > >> Antonio,
> > >> Can you try this. Replace "basename" with one of your RAW/mzXML file
> > >> base name (i.e. <basename>.mzXML)
> > >> This should create basename.pep.xml in the AAS directory. This simple
> > >> exercise is just to confirm that it runs through correctly and the
> > >> process finishes. The next thing to try is to repeat the above data
> > >> structure but try the pepXML conversion in the GUI. Hopefully this
> > >> isolates whether you're experiencing a pepXML conversion problem or a
> > >> GUI problem.
> > >> - Jimmy
> > >> Antonio wrote:
> > >>> Hi Jimmy,
> > >>> I run Sequest from Bioworks on our computer cluster, and then transfer
> > >>> the files to the local machine running TPP, so yeas I had the c:/
> > >>> Inetpub/wwwroot/ISB/data/AAS/test/
> > >>> With the out-and dta- files in it.
> > >>> I have attempted to run Sequest from TPP and I had the same problem;
> > >>> the dta and out files are created, but the command indicates that is
> > >>> still running. The problem occurs whether I send a few files or a
> > >>> single one. But I have more than one file on the queue, the command
> > >>> will not proceed to the next file. I can run Sequest from Bioworks on
> > >>> the local machine without any problems.
> > >>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> > >>>> Antonio,
> > >>>> That warning about not being able to open the mzXML file is not
> > >>>> indicative of the underlying problem. It is truly just a warning and
> > >>>> the analysis process is capable of finishing correctly even if the
> > >>>> corresponding mzXML file is missing.
> > >>>> The important question that's not clear from your description below is
> > >>>> how did you run the Sequest search? Did you run it separately via
> > >>>> Bioworks or did you run the search through the TPP? Although helpful
> > >>>> but not required, it doesn't seem like you did the latter. Do you have
> > >>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has the
> > >>>> Sequest .out files in it?
> > >>>> - Jimmy
> > >>>> Antonio wrote:
> > >>>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
> > >>>>> datafiles from my Sequest search. Now I'm making the corresponding
> > >>>>> pepXML files. I see that the first file is being created, it seems
> > >>>>> that is finished but I see the following warming message at the end of
> > >>>>> the “Output so far” field:
> > >>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
> > >>>>> test.mzXML" for reading MS instrument info and scan times.
> > >>>>> And the command status window indicates that the command is still
> > >>>>> running. Is it? I do not see the file increasing in size. I can open
> > >>>>> the pepxml file, although IE indicates that there is an error on page.
> > >>>>> It seems to me that the program is stuck and is not progressing to
> > >>>>> next task: the creation of the next pepXML file. Solutions?
> > >>>>> Thanks,
> > >>>>> Antonio- Hide quoted text -
> > >>>> - Show quoted text -- Hide quoted text -
> > >> - Show quoted text -- Hide quoted text -
Hi Jimmy,
I have donne it from TPP. the program still gets stuck. pepXML files
are created and Sequest serach is performed, but the program reports
that the command is still running.
I might have a problem with the installation. I will have to reinstall/
rebuild the computer.
Antonio
On Jul 9, 2:41 pm, Antonio <aartig...@kumc.edu> wrote:
> Ok Jimmy,
> Thank you very much for your help.
> I'll repeat the entire process from TPP and I will let you know the
> result.
> Regards,
> Antonio
> On Jul 9, 2:18 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> > I guess the next step is to repeat the pepXML conversion from the GUI
> > and see if the GUI reports that the command completed successfully. If
> > it does, organize a couple of search directories using the same
> > structure and repeat the pepXML conversion. Still getting stuck or is
> > the processes reported to be completed?
> > If if looks like the first pepXML file is generated/completed but the
> > interface thinks the command is still running, I'm going to need Luis to
> > chime in on what to look for as I've exhausted the bits I have knowledge
> > of. So let us know what happens when you try the above.
> > - Jimmy
> > Antonio wrote:
> > > Hi Jimmy,
> > > OK, done it. No problem, the command were successfull, all finished,
> > > th eTPP window indicated that the command was sucessfull and is
> > > finished. i can open the basename.pep on TPP and all seens OK.
> > > What next?
> > > Antonio
> > > On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> > >> Antonio,
> > >> Can you try this. Replace "basename" with one of your RAW/mzXML file
> > >> base name (i.e. <basename>.mzXML)
> > >> This should create basename.pep.xml in the AAS directory. This simple
> > >> exercise is just to confirm that it runs through correctly and the
> > >> process finishes. The next thing to try is to repeat the above data
> > >> structure but try the pepXML conversion in the GUI. Hopefully this
> > >> isolates whether you're experiencing a pepXML conversion problem or a
> > >> GUI problem.
> > >> - Jimmy
> > >> Antonio wrote:
> > >>> Hi Jimmy,
> > >>> I run Sequest from Bioworks on our computer cluster, and then transfer
> > >>> the files to the local machine running TPP, so yeas I had the c:/
> > >>> Inetpub/wwwroot/ISB/data/AAS/test/
> > >>> With the out-and dta- files in it.
> > >>> I have attempted to run Sequest from TPP and I had the same problem;
> > >>> the dta and out files are created, but the command indicates that is
> > >>> still running. The problem occurs whether I send a few files or a
> > >>> single one. But I have more than one file on the queue, the command
> > >>> will not proceed to the next file. I can run Sequest from Bioworks on
> > >>> the local machine without any problems.
> > >>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> > >>>> Antonio,
> > >>>> That warning about not being able to open the mzXML file is not
> > >>>> indicative of the underlying problem. It is truly just a warning and
> > >>>> the analysis process is capable of finishing correctly even if the
> > >>>> corresponding mzXML file is missing.
> > >>>> The important question that's not clear from your description below is
> > >>>> how did you run the Sequest search? Did you run it separately via
> > >>>> Bioworks or did you run the search through the TPP? Although helpful
> > >>>> but not required, it doesn't seem like you did the latter. Do you have
> > >>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has the
> > >>>> Sequest .out files in it?
> > >>>> - Jimmy
> > >>>> Antonio wrote:
> > >>>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
> > >>>>> datafiles from my Sequest search. Now I'm making the corresponding
> > >>>>> pepXML files. I see that the first file is being created, it seems
> > >>>>> that is finished but I see the following warming message at the end of
> > >>>>> the “Output so far” field:
> > >>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
> > >>>>> test.mzXML" for reading MS instrument info and scan times.
> > >>>>> And the command status window indicates that the command is still
> > >>>>> running. Is it? I do not see the file increasing in size. I can open
> > >>>>> the pepxml file, although IE indicates that there is an error on page.
> > >>>>> It seems to me that the program is stuck and is not progressing to
> > >>>>> next task: the creation of the next pepXML file. Solutions?
> > >>>>> Thanks,
> > >>>>> Antonio- Hide quoted text -
> > >>>> - Show quoted text -- Hide quoted text -
> > >> - Show quoted text -- Hide quoted text -
Hopefully Luis or someone else more familiar with the GUI will chime in and help you debug why it appears to not recognize that the pepXML conversions apparently have completed but it still thinks they're running. There are log files somewhere that the GUI looks at that would be the starting point to figuring out your mystery.
Antonio wrote:
> Hi Jimmy,
> I have donne it from TPP. the program still gets stuck. pepXML files
> are created and Sequest serach is performed, but the program reports
> that the command is still running.
> I might have a problem with the installation. I will have to reinstall/
> rebuild the computer.
> Antonio
> On Jul 9, 2:41 pm, Antonio <aartig...@kumc.edu> wrote:
>> Ok Jimmy,
>> Thank you very much for your help.
>> I'll repeat the entire process from TPP and I will let you know the
>> result.
>> Regards,
>> Antonio
>> On Jul 9, 2:18 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>> I guess the next step is to repeat the pepXML conversion from the GUI
>>> and see if the GUI reports that the command completed successfully. If
>>> it does, organize a couple of search directories using the same
>>> structure and repeat the pepXML conversion. Still getting stuck or is
>>> the processes reported to be completed?
>>> If if looks like the first pepXML file is generated/completed but the
>>> interface thinks the command is still running, I'm going to need Luis to
>>> chime in on what to look for as I've exhausted the bits I have knowledge
>>> of. So let us know what happens when you try the above.
>>> - Jimmy
>>> Antonio wrote:
>>>> Hi Jimmy,
>>>> OK, done it. No problem, the command were successfull, all finished,
>>>> th eTPP window indicated that the command was sucessfull and is
>>>> finished. i can open the basename.pep on TPP and all seens OK.
>>>> What next?
>>>> Antonio
>>>> On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>> Antonio,
>>>>> Can you try this. Replace "basename" with one of your RAW/mzXML file
>>>>> base name (i.e. <basename>.mzXML)
>>>>> Collate data as
>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename.mzXML
>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename/ contains dta/out
>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/sequest.params
>>>>> Then in a command prompt run
>>>>> cd c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>> Out2XML basename 1
>>>>> This should create basename.pep.xml in the AAS directory. This simple
>>>>> exercise is just to confirm that it runs through correctly and the
>>>>> process finishes. The next thing to try is to repeat the above data
>>>>> structure but try the pepXML conversion in the GUI. Hopefully this
>>>>> isolates whether you're experiencing a pepXML conversion problem or a
>>>>> GUI problem.
>>>>> - Jimmy
>>>>> Antonio wrote:
>>>>>> Hi Jimmy,
>>>>>> I run Sequest from Bioworks on our computer cluster, and then transfer
>>>>>> the files to the local machine running TPP, so yeas I had the c:/
>>>>>> Inetpub/wwwroot/ISB/data/AAS/test/
>>>>>> With the out-and dta- files in it.
>>>>>> I have attempted to run Sequest from TPP and I had the same problem;
>>>>>> the dta and out files are created, but the command indicates that is
>>>>>> still running. The problem occurs whether I send a few files or a
>>>>>> single one. But I have more than one file on the queue, the command
>>>>>> will not proceed to the next file. I can run Sequest from Bioworks on
>>>>>> the local machine without any problems.
>>>>>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>>> Antonio,
>>>>>>> That warning about not being able to open the mzXML file is not
>>>>>>> indicative of the underlying problem. It is truly just a warning and
>>>>>>> the analysis process is capable of finishing correctly even if the
>>>>>>> corresponding mzXML file is missing.
>>>>>>> The important question that's not clear from your description below is
>>>>>>> how did you run the Sequest search? Did you run it separately via
>>>>>>> Bioworks or did you run the search through the TPP? Although helpful
>>>>>>> but not required, it doesn't seem like you did the latter. Do you have
>>>>>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has the
>>>>>>> Sequest .out files in it?
>>>>>>> - Jimmy
>>>>>>> Antonio wrote:
>>>>>>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
>>>>>>>> datafiles from my Sequest search. Now I'm making the corresponding
>>>>>>>> pepXML files. I see that the first file is being created, it seems
>>>>>>>> that is finished but I see the following warming message at the end of
>>>>>>>> the “Output so far” field:
>>>>>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>>>>> test.mzXML" for reading MS instrument info and scan times.
>>>>>>>> And the command status window indicates that the command is still
>>>>>>>> running. Is it? I do not see the file increasing in size. I can open
>>>>>>>> the pepxml file, although IE indicates that there is an error on page.
>>>>>>>> It seems to me that the program is stuck and is not progressing to
>>>>>>>> next task: the creation of the next pepXML file. Solutions?
>>>>>>>> Thanks,
>>>>>>>> Antonio- Hide quoted text -
>>>>>>> - Show quoted text -- Hide quoted text -
>>>>> - Show quoted text -- Hide quoted text -
>>> - Show quoted text -- Hide quoted text -
>> - Show quoted text -
That can happen on long searches - Apache times out, leaving your session
stuck waiting for a message that never arrives. You can adjust your Apache
config for longer timeouts (look through this group's archives for info on
that).
The next TPP GUI release features a button I added for the user to be able
to tell the GUI "no really, it's done, let's go look at the results".
[mailto:spctools-discuss@googlegroups.com] On Behalf Of Jimmy Eng
Sent: Wednesday, July 15, 2009 10:26 AM
To: spctools-discuss@googlegroups.com
Subject: [spctools-discuss] Re: pepXML
Antonio,
Hopefully Luis or someone else more familiar with the GUI will chime in and help you debug why it appears to not recognize that the pepXML conversions apparently have completed but it still thinks they're running. There are log files somewhere that the GUI looks at that would be the starting point to figuring out your mystery.
- Jimmy
Antonio wrote:
> Hi Jimmy,
> I have donne it from TPP. the program still gets stuck. pepXML files
> are created and Sequest serach is performed, but the program reports
> that the command is still running.
> I might have a problem with the installation. I will have to reinstall/
> rebuild the computer.
> Antonio
> On Jul 9, 2:41 pm, Antonio <aartig...@kumc.edu> wrote:
>> Ok Jimmy,
>> Thank you very much for your help.
>> I'll repeat the entire process from TPP and I will let you know the
>> result.
>> Regards,
>> Antonio
>> On Jul 9, 2:18 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>> I guess the next step is to repeat the pepXML conversion from the GUI
>>> and see if the GUI reports that the command completed successfully. If
>>> it does, organize a couple of search directories using the same
>>> structure and repeat the pepXML conversion. Still getting stuck or is
>>> the processes reported to be completed?
>>> If if looks like the first pepXML file is generated/completed but the
>>> interface thinks the command is still running, I'm going to need Luis to
>>> chime in on what to look for as I've exhausted the bits I have knowledge
>>> of. So let us know what happens when you try the above.
>>> - Jimmy
>>> Antonio wrote:
>>>> Hi Jimmy,
>>>> OK, done it. No problem, the command were successfull, all finished,
>>>> th eTPP window indicated that the command was sucessfull and is
>>>> finished. i can open the basename.pep on TPP and all seens OK.
>>>> What next?
>>>> Antonio
>>>> On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>> Antonio,
>>>>> Can you try this. Replace "basename" with one of your RAW/mzXML file
>>>>> base name (i.e. <basename>.mzXML)
>>>>> Collate data as
>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename.mzXML
>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename/ contains dta/out
>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/sequest.params
>>>>> Then in a command prompt run
>>>>> cd c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>> Out2XML basename 1
>>>>> This should create basename.pep.xml in the AAS directory. This simple
>>>>> exercise is just to confirm that it runs through correctly and the
>>>>> process finishes. The next thing to try is to repeat the above data
>>>>> structure but try the pepXML conversion in the GUI. Hopefully this
>>>>> isolates whether you're experiencing a pepXML conversion problem or a
>>>>> GUI problem.
>>>>> - Jimmy
>>>>> Antonio wrote:
>>>>>> Hi Jimmy,
>>>>>> I run Sequest from Bioworks on our computer cluster, and then
transfer
>>>>>> the files to the local machine running TPP, so yeas I had the c:/
>>>>>> Inetpub/wwwroot/ISB/data/AAS/test/
>>>>>> With the out-and dta- files in it.
>>>>>> I have attempted to run Sequest from TPP and I had the same problem;
>>>>>> the dta and out files are created, but the command indicates that is
>>>>>> still running. The problem occurs whether I send a few files or a
>>>>>> single one. But I have more than one file on the queue, the command
>>>>>> will not proceed to the next file. I can run Sequest from Bioworks on
>>>>>> the local machine without any problems.
>>>>>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>>> Antonio,
>>>>>>> That warning about not being able to open the mzXML file is not
>>>>>>> indicative of the underlying problem. It is truly just a warning
and
>>>>>>> the analysis process is capable of finishing correctly even if the
>>>>>>> corresponding mzXML file is missing.
>>>>>>> The important question that's not clear from your description below
is
>>>>>>> how did you run the Sequest search? Did you run it separately via
>>>>>>> Bioworks or did you run the search through the TPP? Although
helpful
>>>>>>> but not required, it doesn't seem like you did the latter. Do you
have
>>>>>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has
the
>>>>>>> Sequest .out files in it?
>>>>>>> - Jimmy
>>>>>>> Antonio wrote:
>>>>>>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
>>>>>>>> datafiles from my Sequest search. Now I'm making the corresponding
>>>>>>>> pepXML files. I see that the first file is being created, it seems
>>>>>>>> that is finished but I see the following warming message at the end
of
>>>>>>>> the "Output so far" field:
>>>>>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>>>>> test.mzXML" for reading MS instrument info and scan times.
>>>>>>>> And the command status window indicates that the command is still
>>>>>>>> running. Is it? I do not see the file increasing in size. I can
open
>>>>>>>> the pepxml file, although IE indicates that there is an error on
page.
>>>>>>>> It seems to me that the program is stuck and is not progressing to
>>>>>>>> next task: the creation of the next pepXML file. Solutions?
>>>>>>>> Thanks,
>>>>>>>> Antonio- Hide quoted text -
>>>>>>> - Show quoted text -- Hide quoted text -
>>>>> - Show quoted text -- Hide quoted text -
>>> - Show quoted text -- Hide quoted text -
>> - Show quoted text -
It's hard to tell from the dialogue whether the timeout is occuring during the search phase or during the pepXML conversion, which are two different tasks invoked by the GUI. I want to think it's the latter since Antonio mentions that "pepXML conversions apparently have completed". And if this were the case, I'm not sure that Apache time out is the culprit since these conversions shouldn't take forever. Anyways, that looks like a handy feature for the next GUI release.
Brian Pratt wrote:
> That can happen on long searches - Apache times out, leaving your session
> stuck waiting for a message that never arrives. You can adjust your Apache
> config for longer timeouts (look through this group's archives for info on
> that).
> The next TPP GUI release features a button I added for the user to be able
> to tell the GUI "no really, it's done, let's go look at the results".
> -----Original Message-----
> From: spctools-discuss@googlegroups.com
> [mailto:spctools-discuss@googlegroups.com] On Behalf Of Jimmy Eng
> Sent: Wednesday, July 15, 2009 10:26 AM
> To: spctools-discuss@googlegroups.com
> Subject: [spctools-discuss] Re: pepXML
> Antonio,
> Hopefully Luis or someone else more familiar with the GUI will chime in > and help you debug why it appears to not recognize that the pepXML > conversions apparently have completed but it still thinks they're > running. There are log files somewhere that the GUI looks at that would > be the starting point to figuring out your mystery.
> - Jimmy
> Antonio wrote:
>> Hi Jimmy,
>> I have donne it from TPP. the program still gets stuck. pepXML files
>> are created and Sequest serach is performed, but the program reports
>> that the command is still running.
>> I might have a problem with the installation. I will have to reinstall/
>> rebuild the computer.
>> Antonio
>> On Jul 9, 2:41 pm, Antonio <aartig...@kumc.edu> wrote:
>>> Ok Jimmy,
>>> Thank you very much for your help.
>>> I'll repeat the entire process from TPP and I will let you know the
>>> result.
>>> Regards,
>>> Antonio
>>> On Jul 9, 2:18 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>> I guess the next step is to repeat the pepXML conversion from the GUI
>>>> and see if the GUI reports that the command completed successfully. If
>>>> it does, organize a couple of search directories using the same
>>>> structure and repeat the pepXML conversion. Still getting stuck or is
>>>> the processes reported to be completed?
>>>> If if looks like the first pepXML file is generated/completed but the
>>>> interface thinks the command is still running, I'm going to need Luis to
>>>> chime in on what to look for as I've exhausted the bits I have knowledge
>>>> of. So let us know what happens when you try the above.
>>>> - Jimmy
>>>> Antonio wrote:
>>>>> Hi Jimmy,
>>>>> OK, done it. No problem, the command were successfull, all finished,
>>>>> th eTPP window indicated that the command was sucessfull and is
>>>>> finished. i can open the basename.pep on TPP and all seens OK.
>>>>> What next?
>>>>> Antonio
>>>>> On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>> Antonio,
>>>>>> Can you try this. Replace "basename" with one of your RAW/mzXML file
>>>>>> base name (i.e. <basename>.mzXML)
>>>>>> Collate data as
>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename.mzXML
>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename/ contains dta/out
>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/sequest.params
>>>>>> Then in a command prompt run
>>>>>> cd c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>>> Out2XML basename 1
>>>>>> This should create basename.pep.xml in the AAS directory. This simple
>>>>>> exercise is just to confirm that it runs through correctly and the
>>>>>> process finishes. The next thing to try is to repeat the above data
>>>>>> structure but try the pepXML conversion in the GUI. Hopefully this
>>>>>> isolates whether you're experiencing a pepXML conversion problem or a
>>>>>> GUI problem.
>>>>>> - Jimmy
>>>>>> Antonio wrote:
>>>>>>> Hi Jimmy,
>>>>>>> I run Sequest from Bioworks on our computer cluster, and then
> transfer
>>>>>>> the files to the local machine running TPP, so yeas I had the c:/
>>>>>>> Inetpub/wwwroot/ISB/data/AAS/test/
>>>>>>> With the out-and dta- files in it.
>>>>>>> I have attempted to run Sequest from TPP and I had the same problem;
>>>>>>> the dta and out files are created, but the command indicates that is
>>>>>>> still running. The problem occurs whether I send a few files or a
>>>>>>> single one. But I have more than one file on the queue, the command
>>>>>>> will not proceed to the next file. I can run Sequest from Bioworks on
>>>>>>> the local machine without any problems.
>>>>>>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>>>> Antonio,
>>>>>>>> That warning about not being able to open the mzXML file is not
>>>>>>>> indicative of the underlying problem. It is truly just a warning
> and
>>>>>>>> the analysis process is capable of finishing correctly even if the
>>>>>>>> corresponding mzXML file is missing.
>>>>>>>> The important question that's not clear from your description below
> is
>>>>>>>> how did you run the Sequest search? Did you run it separately via
>>>>>>>> Bioworks or did you run the search through the TPP? Although
> helpful
>>>>>>>> but not required, it doesn't seem like you did the latter. Do you
> have
>>>>>>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has
> the
>>>>>>>> Sequest .out files in it?
>>>>>>>> - Jimmy
>>>>>>>> Antonio wrote:
>>>>>>>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
>>>>>>>>> datafiles from my Sequest search. Now I'm making the corresponding
>>>>>>>>> pepXML files. I see that the first file is being created, it seems
>>>>>>>>> that is finished but I see the following warming message at the end
> of
>>>>>>>>> the "Output so far" field:
>>>>>>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>>>>>> test.mzXML" for reading MS instrument info and scan times.
>>>>>>>>> And the command status window indicates that the command is still
>>>>>>>>> running. Is it? I do not see the file increasing in size. I can
> open
>>>>>>>>> the pepxml file, although IE indicates that there is an error on
> page.
>>>>>>>>> It seems to me that the program is stuck and is not progressing to
>>>>>>>>> next task: the creation of the next pepXML file. Solutions?
>>>>>>>>> Thanks,
>>>>>>>>> Antonio- Hide quoted text -
>>>>>>>> - Show quoted text -- Hide quoted text -
>>>>>> - Show quoted text -- Hide quoted text -
>>>> - Show quoted text -- Hide quoted text -
>>> - Show quoted text -
Agreed - the proper test is to invoke it from the command line and see if it
actually does complete eventually. An infinite loop bug is always a
possibility.
[mailto:spctools-discuss@googlegroups.com] On Behalf Of Jimmy Eng
Sent: Wednesday, July 15, 2009 1:02 PM
To: spctools-discuss@googlegroups.com
Subject: [spctools-discuss] Re: pepXML
It's hard to tell from the dialogue whether the timeout is occuring during the search phase or during the pepXML conversion, which are two different tasks invoked by the GUI. I want to think it's the latter since Antonio mentions that "pepXML conversions apparently have completed". And if this were the case, I'm not sure that Apache time out is the culprit since these conversions shouldn't take forever. Anyways, that looks like a handy feature for the next GUI release.
Brian Pratt wrote:
> That can happen on long searches - Apache times out, leaving your session
> stuck waiting for a message that never arrives. You can adjust your
Apache
> config for longer timeouts (look through this group's archives for info on
> that).
> The next TPP GUI release features a button I added for the user to be able
> to tell the GUI "no really, it's done, let's go look at the results".
> -----Original Message-----
> From: spctools-discuss@googlegroups.com
> [mailto:spctools-discuss@googlegroups.com] On Behalf Of Jimmy Eng
> Sent: Wednesday, July 15, 2009 10:26 AM
> To: spctools-discuss@googlegroups.com
> Subject: [spctools-discuss] Re: pepXML
> Antonio,
> Hopefully Luis or someone else more familiar with the GUI will chime in > and help you debug why it appears to not recognize that the pepXML > conversions apparently have completed but it still thinks they're > running. There are log files somewhere that the GUI looks at that would > be the starting point to figuring out your mystery.
> - Jimmy
> Antonio wrote:
>> Hi Jimmy,
>> I have donne it from TPP. the program still gets stuck. pepXML files
>> are created and Sequest serach is performed, but the program reports
>> that the command is still running.
>> I might have a problem with the installation. I will have to reinstall/
>> rebuild the computer.
>> Antonio
>> On Jul 9, 2:41 pm, Antonio <aartig...@kumc.edu> wrote:
>>> Ok Jimmy,
>>> Thank you very much for your help.
>>> I'll repeat the entire process from TPP and I will let you know the
>>> result.
>>> Regards,
>>> Antonio
>>> On Jul 9, 2:18 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>> I guess the next step is to repeat the pepXML conversion from the GUI
>>>> and see if the GUI reports that the command completed successfully. If
>>>> it does, organize a couple of search directories using the same
>>>> structure and repeat the pepXML conversion. Still getting stuck or is
>>>> the processes reported to be completed?
>>>> If if looks like the first pepXML file is generated/completed but the
>>>> interface thinks the command is still running, I'm going to need Luis
to
>>>> chime in on what to look for as I've exhausted the bits I have
knowledge
>>>> of. So let us know what happens when you try the above.
>>>> - Jimmy
>>>> Antonio wrote:
>>>>> Hi Jimmy,
>>>>> OK, done it. No problem, the command were successfull, all finished,
>>>>> th eTPP window indicated that the command was sucessfull and is
>>>>> finished. i can open the basename.pep on TPP and all seens OK.
>>>>> What next?
>>>>> Antonio
>>>>> On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>> Antonio,
>>>>>> Can you try this. Replace "basename" with one of your RAW/mzXML file
>>>>>> base name (i.e. <basename>.mzXML)
>>>>>> Collate data as
>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename.mzXML
>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename/ contains dta/out
>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/sequest.params
>>>>>> Then in a command prompt run
>>>>>> cd c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>>> Out2XML basename 1
>>>>>> This should create basename.pep.xml in the AAS directory. This
simple
>>>>>> exercise is just to confirm that it runs through correctly and the
>>>>>> process finishes. The next thing to try is to repeat the above data
>>>>>> structure but try the pepXML conversion in the GUI. Hopefully this
>>>>>> isolates whether you're experiencing a pepXML conversion problem or a
>>>>>> GUI problem.
>>>>>> - Jimmy
>>>>>> Antonio wrote:
>>>>>>> Hi Jimmy,
>>>>>>> I run Sequest from Bioworks on our computer cluster, and then
> transfer
>>>>>>> the files to the local machine running TPP, so yeas I had the c:/
>>>>>>> Inetpub/wwwroot/ISB/data/AAS/test/
>>>>>>> With the out-and dta- files in it.
>>>>>>> I have attempted to run Sequest from TPP and I had the same problem;
>>>>>>> the dta and out files are created, but the command indicates that is
>>>>>>> still running. The problem occurs whether I send a few files or a
>>>>>>> single one. But I have more than one file on the queue, the command
>>>>>>> will not proceed to the next file. I can run Sequest from Bioworks
on
>>>>>>> the local machine without any problems.
>>>>>>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>>>> Antonio,
>>>>>>>> That warning about not being able to open the mzXML file is not
>>>>>>>> indicative of the underlying problem. It is truly just a warning
> and
>>>>>>>> the analysis process is capable of finishing correctly even if the
>>>>>>>> corresponding mzXML file is missing.
>>>>>>>> The important question that's not clear from your description below
> is
>>>>>>>> how did you run the Sequest search? Did you run it separately via
>>>>>>>> Bioworks or did you run the search through the TPP? Although
> helpful
>>>>>>>> but not required, it doesn't seem like you did the latter. Do you
> have
>>>>>>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has
> the
>>>>>>>> Sequest .out files in it?
>>>>>>>> - Jimmy
>>>>>>>> Antonio wrote:
>>>>>>>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
>>>>>>>>> datafiles from my Sequest search. Now I'm making the corresponding
>>>>>>>>> pepXML files. I see that the first file is being created, it seems
>>>>>>>>> that is finished but I see the following warming message at the
end
> of
>>>>>>>>> the "Output so far" field:
>>>>>>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>>>>>> test.mzXML" for reading MS instrument info and scan times.
>>>>>>>>> And the command status window indicates that the command is still
>>>>>>>>> running. Is it? I do not see the file increasing in size. I can
> open
>>>>>>>>> the pepxml file, although IE indicates that there is an error on
> page.
>>>>>>>>> It seems to me that the program is stuck and is not progressing to
>>>>>>>>> next task: the creation of the next pepXML file. Solutions?
>>>>>>>>> Thanks,
>>>>>>>>> Antonio- Hide quoted text -
>>>>>>>> - Show quoted text -- Hide quoted text -
>>>>>> - Show quoted text -- Hide quoted text -
>>>> - Show quoted text -- Hide quoted text -
>>> - Show quoted text -
Brian Pratt wrote:
> Agreed - the proper test is to invoke it from the command line and see if it
> actually does complete eventually. An infinite loop bug is always a
> possibility.
> Brian
> -----Original Message-----
> From: spctools-discuss@googlegroups.com
> [mailto:spctools-discuss@googlegroups.com] On Behalf Of Jimmy Eng
> Sent: Wednesday, July 15, 2009 1:02 PM
> To: spctools-discuss@googlegroups.com
> Subject: [spctools-discuss] Re: pepXML
> It's hard to tell from the dialogue whether the timeout is occuring > during the search phase or during the pepXML conversion, which are two > different tasks invoked by the GUI. I want to think it's the latter > since Antonio mentions that "pepXML conversions apparently have > completed". And if this were the case, I'm not sure that Apache time > out is the culprit since these conversions shouldn't take forever. > Anyways, that looks like a handy feature for the next GUI release.
> Brian Pratt wrote:
>> That can happen on long searches - Apache times out, leaving your session
>> stuck waiting for a message that never arrives. You can adjust your
> Apache
>> config for longer timeouts (look through this group's archives for info on
>> that).
>> The next TPP GUI release features a button I added for the user to be able
>> to tell the GUI "no really, it's done, let's go look at the results".
>> -----Original Message-----
>> From: spctools-discuss@googlegroups.com
>> [mailto:spctools-discuss@googlegroups.com] On Behalf Of Jimmy Eng
>> Sent: Wednesday, July 15, 2009 10:26 AM
>> To: spctools-discuss@googlegroups.com
>> Subject: [spctools-discuss] Re: pepXML
>> Antonio,
>> Hopefully Luis or someone else more familiar with the GUI will chime in >> and help you debug why it appears to not recognize that the pepXML >> conversions apparently have completed but it still thinks they're >> running. There are log files somewhere that the GUI looks at that would >> be the starting point to figuring out your mystery.
>> - Jimmy
>> Antonio wrote:
>>> Hi Jimmy,
>>> I have donne it from TPP. the program still gets stuck. pepXML files
>>> are created and Sequest serach is performed, but the program reports
>>> that the command is still running.
>>> I might have a problem with the installation. I will have to reinstall/
>>> rebuild the computer.
>>> Antonio
>>> On Jul 9, 2:41 pm, Antonio <aartig...@kumc.edu> wrote:
>>>> Ok Jimmy,
>>>> Thank you very much for your help.
>>>> I'll repeat the entire process from TPP and I will let you know the
>>>> result.
>>>> Regards,
>>>> Antonio
>>>> On Jul 9, 2:18 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>> I guess the next step is to repeat the pepXML conversion from the GUI
>>>>> and see if the GUI reports that the command completed successfully. If
>>>>> it does, organize a couple of search directories using the same
>>>>> structure and repeat the pepXML conversion. Still getting stuck or is
>>>>> the processes reported to be completed?
>>>>> If if looks like the first pepXML file is generated/completed but the
>>>>> interface thinks the command is still running, I'm going to need Luis
> to
>>>>> chime in on what to look for as I've exhausted the bits I have
> knowledge
>>>>> of. So let us know what happens when you try the above.
>>>>> - Jimmy
>>>>> Antonio wrote:
>>>>>> Hi Jimmy,
>>>>>> OK, done it. No problem, the command were successfull, all finished,
>>>>>> th eTPP window indicated that the command was sucessfull and is
>>>>>> finished. i can open the basename.pep on TPP and all seens OK.
>>>>>> What next?
>>>>>> Antonio
>>>>>> On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>>> Antonio,
>>>>>>> Can you try this. Replace "basename" with one of your RAW/mzXML file
>>>>>>> base name (i.e. <basename>.mzXML)
>>>>>>> Collate data as
>>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename.mzXML
>>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename/ contains dta/out
>>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/sequest.params
>>>>>>> Then in a command prompt run
>>>>>>> cd c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>>>> Out2XML basename 1
>>>>>>> This should create basename.pep.xml in the AAS directory. This
> simple
>>>>>>> exercise is just to confirm that it runs through correctly and the
>>>>>>> process finishes. The next thing to try is to repeat the above data
>>>>>>> structure but try the pepXML conversion in the GUI. Hopefully this
>>>>>>> isolates whether you're experiencing a pepXML conversion problem or a
>>>>>>> GUI problem.
>>>>>>> - Jimmy
>>>>>>> Antonio wrote:
>>>>>>>> Hi Jimmy,
>>>>>>>> I run Sequest from Bioworks on our computer cluster, and then
>> transfer
>>>>>>>> the files to the local machine running TPP, so yeas I had the c:/
>>>>>>>> Inetpub/wwwroot/ISB/data/AAS/test/
>>>>>>>> With the out-and dta- files in it.
>>>>>>>> I have attempted to run Sequest from TPP and I had the same problem;
>>>>>>>> the dta and out files are created, but the command indicates that is
>>>>>>>> still running. The problem occurs whether I send a few files or a
>>>>>>>> single one. But I have more than one file on the queue, the command
>>>>>>>> will not proceed to the next file. I can run Sequest from Bioworks
> on
>>>>>>>> the local machine without any problems.
>>>>>>>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>>>>> Antonio,
>>>>>>>>> That warning about not being able to open the mzXML file is not
>>>>>>>>> indicative of the underlying problem. It is truly just a warning
>> and
>>>>>>>>> the analysis process is capable of finishing correctly even if the
>>>>>>>>> corresponding mzXML file is missing.
>>>>>>>>> The important question that's not clear from your description below
>> is
>>>>>>>>> how did you run the Sequest search? Did you run it separately via
>>>>>>>>> Bioworks or did you run the search through the TPP? Although
>> helpful
>>>>>>>>> but not required, it doesn't seem like you did the latter. Do you
>> have
>>>>>>>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has
>> the
>>>>>>>>> Sequest .out files in it?
>>>>>>>>> - Jimmy
>>>>>>>>> Antonio wrote:
>>>>>>>>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
>>>>>>>>>> datafiles from my Sequest search. Now I'm making the corresponding
>>>>>>>>>> pepXML files. I see that the first file is being created, it seems
>>>>>>>>>> that is finished but I see the following warming message at the
> end
>> of
>>>>>>>>>> the "Output so far" field:
>>>>>>>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>>>>>>> test.mzXML" for reading MS instrument info and scan times.
>>>>>>>>>> And the command status window indicates that the command is still
>>>>>>>>>> running. Is it? I do not see the file increasing in size. I can
>> open
>>>>>>>>>> the pepxml file, although IE indicates that there is an error on
>> page.
>>>>>>>>>> It seems to me that the program is stuck and is not progressing to
>>>>>>>>>> next task: the creation of the next pepXML file. Solutions?
>>>>>>>>>> Thanks,
>>>>>>>>>> Antonio- Hide quoted text -
>>>>>>>>> - Show quoted text -- Hide quoted text -
>>>>>>> - Show quoted text -- Hide quoted text -
>>>>> - Show quoted text -- Hide quoted text -
>>>> - Show quoted text -
Jimmy,
Just to clarify: the timeout occurs both during the Sequest search and
also during the pepXML conversion. I haven't gotten the time to
reinstall the software in this computer; I hope I can do it sometime
this week.
I'll post my findings once this is completed.
Again, many thanks you for your help,
Antonio
On Jul 15, 3:02 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> It's hard to tell from the dialogue whether the timeout is occuring
> during the search phase or during the pepXML conversion, which are two
> different tasks invoked by the GUI. I want to think it's the latter
> since Antonio mentions that "pepXML conversions apparently have
> completed". And if this were the case, I'm not sure that Apache time
> out is the culprit since these conversions shouldn't take forever.
> Anyways, that looks like a handy feature for the next GUI release.
> Brian Pratt wrote:
> > That can happen on long searches - Apache times out, leaving your session
> > stuck waiting for a message that never arrives. You can adjust your Apache
> > config for longer timeouts (look through this group's archives for info on
> > that).
> > The next TPP GUI release features a button I added for the user to be able
> > to tell the GUI "no really, it's done, let's go look at the results".
> > -----Original Message-----
> > From: spctools-discuss@googlegroups.com
> > [mailto:spctools-discuss@googlegroups.com] On Behalf Of Jimmy Eng
> > Sent: Wednesday, July 15, 2009 10:26 AM
> > To: spctools-discuss@googlegroups.com
> > Subject: [spctools-discuss] Re: pepXML
> > Antonio,
> > Hopefully Luis or someone else more familiar with the GUI will chime in
> > and help you debug why it appears to not recognize that the pepXML
> > conversions apparently have completed but it still thinks they're
> > running. There are log files somewhere that the GUI looks at that would
> > be the starting point to figuring out your mystery.
> > - Jimmy
> > Antonio wrote:
> >> Hi Jimmy,
> >> I have donne it from TPP. the program still gets stuck. pepXML files
> >> are created and Sequest serach is performed, but the program reports
> >> that the command is still running.
> >> I might have a problem with the installation. I will have to reinstall/
> >> rebuild the computer.
> >> Antonio
> >> On Jul 9, 2:41 pm, Antonio <aartig...@kumc.edu> wrote:
> >>> Ok Jimmy,
> >>> Thank you very much for your help.
> >>> I'll repeat the entire process from TPP and I will let you know the
> >>> result.
> >>> Regards,
> >>> Antonio
> >>> On Jul 9, 2:18 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> >>>> I guess the next step is to repeat the pepXML conversion from the GUI
> >>>> and see if the GUI reports that the command completed successfully. If
> >>>> it does, organize a couple of search directories using the same
> >>>> structure and repeat the pepXML conversion. Still getting stuck or is
> >>>> the processes reported to be completed?
> >>>> If if looks like the first pepXML file is generated/completed but the
> >>>> interface thinks the command is still running, I'm going to need Luis to
> >>>> chime in on what to look for as I've exhausted the bits I have knowledge
> >>>> of. So let us know what happens when you try the above.
> >>>> - Jimmy
> >>>> Antonio wrote:
> >>>>> Hi Jimmy,
> >>>>> OK, done it. No problem, the command were successfull, all finished,
> >>>>> th eTPP window indicated that the command was sucessfull and is
> >>>>> finished. i can open the basename.pep on TPP and all seens OK.
> >>>>> What next?
> >>>>> Antonio
> >>>>> On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> >>>>>> Antonio,
> >>>>>> Can you try this. Replace "basename" with one of your RAW/mzXML file
> >>>>>> base name (i.e. <basename>.mzXML)
> >>>>>> Collate data as
> >>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename.mzXML
> >>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename/ contains dta/out
> >>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/sequest.params
> >>>>>> Then in a command prompt run
> >>>>>> cd c:/Inetpub/wwwroot/ISB/data/AAS/
> >>>>>> Out2XML basename 1
> >>>>>> This should create basename.pep.xml in the AAS directory. This simple
> >>>>>> exercise is just to confirm that it runs through correctly and the
> >>>>>> process finishes. The next thing to try is to repeat the above data
> >>>>>> structure but try the pepXML conversion in the GUI. Hopefully this
> >>>>>> isolates whether you're experiencing a pepXML conversion problem or a
> >>>>>> GUI problem.
> >>>>>> - Jimmy
> >>>>>> Antonio wrote:
> >>>>>>> Hi Jimmy,
> >>>>>>> I run Sequest from Bioworks on our computer cluster, and then
> > transfer
> >>>>>>> the files to the local machine running TPP, so yeas I had the c:/
> >>>>>>> Inetpub/wwwroot/ISB/data/AAS/test/
> >>>>>>> With the out-and dta- files in it.
> >>>>>>> I have attempted to run Sequest from TPP and I had the same problem;
> >>>>>>> the dta and out files are created, but the command indicates that is
> >>>>>>> still running. The problem occurs whether I send a few files or a
> >>>>>>> single one. But I have more than one file on the queue, the command
> >>>>>>> will not proceed to the next file. I can run Sequest from Bioworks on
> >>>>>>> the local machine without any problems.
> >>>>>>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
> >>>>>>>> Antonio,
> >>>>>>>> That warning about not being able to open the mzXML file is not
> >>>>>>>> indicative of the underlying problem. It is truly just a warning
> > and
> >>>>>>>> the analysis process is capable of finishing correctly even if the
> >>>>>>>> corresponding mzXML file is missing.
> >>>>>>>> The important question that's not clear from your description below
> > is
> >>>>>>>> how did you run the Sequest search? Did you run it separately via
> >>>>>>>> Bioworks or did you run the search through the TPP? Although
> > helpful
> >>>>>>>> but not required, it doesn't seem like you did the latter. Do you
> > have
> >>>>>>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has
> > the
> >>>>>>>> Sequest .out files in it?
> >>>>>>>> - Jimmy
> >>>>>>>> Antonio wrote:
> >>>>>>>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
> >>>>>>>>> datafiles from my Sequest search. Now I'm making the corresponding
> >>>>>>>>> pepXML files. I see that the first file is being created, it seems
> >>>>>>>>> that is finished but I see the following warming message at the end
> > of
> >>>>>>>>> the "Output so far" field:
> >>>>>>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
> >>>>>>>>> test.mzXML" for reading MS instrument info and scan times.
> >>>>>>>>> And the command status window indicates that the command is still
> >>>>>>>>> running. Is it? I do not see the file increasing in size. I can
> > open
> >>>>>>>>> the pepxml file, although IE indicates that there is an error on
> > page.
> >>>>>>>>> It seems to me that the program is stuck and is not progressing to
> >>>>>>>>> next task: the creation of the next pepXML file. Solutions?
> >>>>>>>>> Thanks,
> >>>>>>>>> Antonio- Hide quoted text -
> >>>>>>>> - Show quoted text -- Hide quoted text -
> >>>>>> - Show quoted text -- Hide quoted text -
> >>>> - Show quoted text -- Hide quoted text -
> >>> - Show quoted text -
A search for 'apache timeout' in this google group brings up this thread with some information on how to change that parameter:
http://tinyurl.com/nrr58v
Antonio wrote:
> Jimmy,
> Just to clarify: the timeout occurs both during the Sequest search and
> also during the pepXML conversion. I haven't gotten the time to
> reinstall the software in this computer; I hope I can do it sometime
> this week.
> I'll post my findings once this is completed.
> Again, many thanks you for your help,
> Antonio
> On Jul 15, 3:02 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>> It's hard to tell from the dialogue whether the timeout is occuring
>> during the search phase or during the pepXML conversion, which are two
>> different tasks invoked by the GUI. I want to think it's the latter
>> since Antonio mentions that "pepXML conversions apparently have
>> completed". And if this were the case, I'm not sure that Apache time
>> out is the culprit since these conversions shouldn't take forever.
>> Anyways, that looks like a handy feature for the next GUI release.
>> Brian Pratt wrote:
>>> That can happen on long searches - Apache times out, leaving your session
>>> stuck waiting for a message that never arrives. You can adjust your Apache
>>> config for longer timeouts (look through this group's archives for info on
>>> that).
>>> The next TPP GUI release features a button I added for the user to be able
>>> to tell the GUI "no really, it's done, let's go look at the results".
>>> -----Original Message-----
>>> From: spctools-discuss@googlegroups.com
>>> [mailto:spctools-discuss@googlegroups.com] On Behalf Of Jimmy Eng
>>> Sent: Wednesday, July 15, 2009 10:26 AM
>>> To: spctools-discuss@googlegroups.com
>>> Subject: [spctools-discuss] Re: pepXML
>>> Antonio,
>>> Hopefully Luis or someone else more familiar with the GUI will chime in
>>> and help you debug why it appears to not recognize that the pepXML
>>> conversions apparently have completed but it still thinks they're
>>> running. There are log files somewhere that the GUI looks at that would
>>> be the starting point to figuring out your mystery.
>>> - Jimmy
>>> Antonio wrote:
>>>> Hi Jimmy,
>>>> I have donne it from TPP. the program still gets stuck. pepXML files
>>>> are created and Sequest serach is performed, but the program reports
>>>> that the command is still running.
>>>> I might have a problem with the installation. I will have to reinstall/
>>>> rebuild the computer.
>>>> Antonio
>>>> On Jul 9, 2:41 pm, Antonio <aartig...@kumc.edu> wrote:
>>>>> Ok Jimmy,
>>>>> Thank you very much for your help.
>>>>> I'll repeat the entire process from TPP and I will let you know the
>>>>> result.
>>>>> Regards,
>>>>> Antonio
>>>>> On Jul 9, 2:18 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>> I guess the next step is to repeat the pepXML conversion from the GUI
>>>>>> and see if the GUI reports that the command completed successfully. If
>>>>>> it does, organize a couple of search directories using the same
>>>>>> structure and repeat the pepXML conversion. Still getting stuck or is
>>>>>> the processes reported to be completed?
>>>>>> If if looks like the first pepXML file is generated/completed but the
>>>>>> interface thinks the command is still running, I'm going to need Luis to
>>>>>> chime in on what to look for as I've exhausted the bits I have knowledge
>>>>>> of. So let us know what happens when you try the above.
>>>>>> - Jimmy
>>>>>> Antonio wrote:
>>>>>>> Hi Jimmy,
>>>>>>> OK, done it. No problem, the command were successfull, all finished,
>>>>>>> th eTPP window indicated that the command was sucessfull and is
>>>>>>> finished. i can open the basename.pep on TPP and all seens OK.
>>>>>>> What next?
>>>>>>> Antonio
>>>>>>> On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>>>> Antonio,
>>>>>>>> Can you try this. Replace "basename" with one of your RAW/mzXML file
>>>>>>>> base name (i.e. <basename>.mzXML)
>>>>>>>> Collate data as
>>>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename.mzXML
>>>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename/ contains dta/out
>>>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/sequest.params
>>>>>>>> Then in a command prompt run
>>>>>>>> cd c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>>>>> Out2XML basename 1
>>>>>>>> This should create basename.pep.xml in the AAS directory. This simple
>>>>>>>> exercise is just to confirm that it runs through correctly and the
>>>>>>>> process finishes. The next thing to try is to repeat the above data
>>>>>>>> structure but try the pepXML conversion in the GUI. Hopefully this
>>>>>>>> isolates whether you're experiencing a pepXML conversion problem or a
>>>>>>>> GUI problem.
>>>>>>>> - Jimmy
>>>>>>>> Antonio wrote:
>>>>>>>>> Hi Jimmy,
>>>>>>>>> I run Sequest from Bioworks on our computer cluster, and then
>>> transfer
>>>>>>>>> the files to the local machine running TPP, so yeas I had the c:/
>>>>>>>>> Inetpub/wwwroot/ISB/data/AAS/test/
>>>>>>>>> With the out-and dta- files in it.
>>>>>>>>> I have attempted to run Sequest from TPP and I had the same problem;
>>>>>>>>> the dta and out files are created, but the command indicates that is
>>>>>>>>> still running. The problem occurs whether I send a few files or a
>>>>>>>>> single one. But I have more than one file on the queue, the command
>>>>>>>>> will not proceed to the next file. I can run Sequest from Bioworks on
>>>>>>>>> the local machine without any problems.
>>>>>>>>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>>>>>> Antonio,
>>>>>>>>>> That warning about not being able to open the mzXML file is not
>>>>>>>>>> indicative of the underlying problem. It is truly just a warning
>>> and
>>>>>>>>>> the analysis process is capable of finishing correctly even if the
>>>>>>>>>> corresponding mzXML file is missing.
>>>>>>>>>> The important question that's not clear from your description below
>>> is
>>>>>>>>>> how did you run the Sequest search? Did you run it separately via
>>>>>>>>>> Bioworks or did you run the search through the TPP? Although
>>> helpful
>>>>>>>>>> but not required, it doesn't seem like you did the latter. Do you
>>> have
>>>>>>>>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has
>>> the
>>>>>>>>>> Sequest .out files in it?
>>>>>>>>>> - Jimmy
>>>>>>>>>> Antonio wrote:
>>>>>>>>>>> I have installed TPP v4.2 on windows XP. I have created the mzXML
>>>>>>>>>>> datafiles from my Sequest search. Now I'm making the corresponding
>>>>>>>>>>> pepXML files. I see that the first file is being created, it seems
>>>>>>>>>>> that is finished but I see the following warming message at the end
>>> of
>>>>>>>>>>> the "Output so far" field:
>>>>>>>>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>>>>>>>> test.mzXML" for reading MS instrument info and scan times.
>>>>>>>>>>> And the command status window indicates that the command is still
>>>>>>>>>>> running. Is it? I do not see the file increasing in size. I can
>>> open
>>>>>>>>>>> the pepxml file, although IE indicates that there is an error on
>>> page.
>>>>>>>>>>> It seems to me that the program is stuck and is not progressing to
>>>>>>>>>>> next task: the creation of the next pepXML file. Solutions?
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Antonio- Hide quoted text -
>>>>>>>>>> - Show quoted text -- Hide quoted text -
>>>>>>>> - Show quoted text -- Hide quoted text -
>>>>>> - Show quoted text -- Hide quoted text -
>>>>> - Show quoted text -
Also, note that if you want the TPP installation to set this for you,
you'll want to uninstall Apache first. If the TPP installer detects
that you have Apache already running, it won't change the configuration.
> A search for 'apache timeout' in this google group brings up this
> thread
> with some information on how to change that parameter:
> http://tinyurl.com/nrr58v
> - Jimmy
> Antonio wrote:
>> Jimmy,
>> Just to clarify: the timeout occurs both during the Sequest search
>> and
>> also during the pepXML conversion. I haven't gotten the time to
>> reinstall the software in this computer; I hope I can do it sometime
>> this week.
>> I'll post my findings once this is completed.
>> Again, many thanks you for your help,
>> Antonio
>> On Jul 15, 3:02 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>> It's hard to tell from the dialogue whether the timeout is occuring
>>> during the search phase or during the pepXML conversion, which are
>>> two
>>> different tasks invoked by the GUI. I want to think it's the latter
>>> since Antonio mentions that "pepXML conversions apparently have
>>> completed". And if this were the case, I'm not sure that Apache
>>> time
>>> out is the culprit since these conversions shouldn't take forever.
>>> Anyways, that looks like a handy feature for the next GUI release.
>>> Brian Pratt wrote:
>>>> That can happen on long searches - Apache times out, leaving your
>>>> session
>>>> stuck waiting for a message that never arrives. You can adjust
>>>> your Apache
>>>> config for longer timeouts (look through this group's archives
>>>> for info on
>>>> that).
>>>> The next TPP GUI release features a button I added for the user
>>>> to be able
>>>> to tell the GUI "no really, it's done, let's go look at the
>>>> results".
>>>> -----Original Message-----
>>>> From: spctools-discuss@googlegroups.com
>>>> [mailto:spctools-discuss@googlegroups.com] On Behalf Of Jimmy Eng
>>>> Sent: Wednesday, July 15, 2009 10:26 AM
>>>> To: spctools-discuss@googlegroups.com
>>>> Subject: [spctools-discuss] Re: pepXML
>>>> Antonio,
>>>> Hopefully Luis or someone else more familiar with the GUI will
>>>> chime in
>>>> and help you debug why it appears to not recognize that the pepXML
>>>> conversions apparently have completed but it still thinks they're
>>>> running. There are log files somewhere that the GUI looks at
>>>> that would
>>>> be the starting point to figuring out your mystery.
>>>> - Jimmy
>>>> Antonio wrote:
>>>>> Hi Jimmy,
>>>>> I have donne it from TPP. the program still gets stuck. pepXML
>>>>> files
>>>>> are created and Sequest serach is performed, but the program
>>>>> reports
>>>>> that the command is still running.
>>>>> I might have a problem with the installation. I will have to
>>>>> reinstall/
>>>>> rebuild the computer.
>>>>> Antonio
>>>>> On Jul 9, 2:41 pm, Antonio <aartig...@kumc.edu> wrote:
>>>>>> Ok Jimmy,
>>>>>> Thank you very much for your help.
>>>>>> I'll repeat the entire process from TPP and I will let you know
>>>>>> the
>>>>>> result.
>>>>>> Regards,
>>>>>> Antonio
>>>>>> On Jul 9, 2:18 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>>> I guess the next step is to repeat the pepXML conversion from
>>>>>>> the GUI
>>>>>>> and see if the GUI reports that the command completed
>>>>>>> successfully. If
>>>>>>> it does, organize a couple of search directories using the same
>>>>>>> structure and repeat the pepXML conversion. Still getting
>>>>>>> stuck or is
>>>>>>> the processes reported to be completed?
>>>>>>> If if looks like the first pepXML file is generated/completed
>>>>>>> but the
>>>>>>> interface thinks the command is still running, I'm going to
>>>>>>> need Luis to
>>>>>>> chime in on what to look for as I've exhausted the bits I have
>>>>>>> knowledge
>>>>>>> of. So let us know what happens when you try the above.
>>>>>>> - Jimmy
>>>>>>> Antonio wrote:
>>>>>>>> Hi Jimmy,
>>>>>>>> OK, done it. No problem, the command were successfull, all
>>>>>>>> finished,
>>>>>>>> th eTPP window indicated that the command was sucessfull and is
>>>>>>>> finished. i can open the basename.pep on TPP and all seens OK.
>>>>>>>> What next?
>>>>>>>> Antonio
>>>>>>>> On Jul 8, 12:33 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>>>>> Antonio,
>>>>>>>>> Can you try this. Replace "basename" with one of your RAW/ >>>>>>>>> mzXML file
>>>>>>>>> base name (i.e. <basename>.mzXML)
>>>>>>>>> Collate data as
>>>>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename.mzXML
>>>>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/basename/ contains dta/out
>>>>>>>>> c:/Inetpub/wwwroot/ISB/data/AAS/sequest.params
>>>>>>>>> Then in a command prompt run
>>>>>>>>> cd c:/Inetpub/wwwroot/ISB/data/AAS/
>>>>>>>>> Out2XML basename 1
>>>>>>>>> This should create basename.pep.xml in the AAS directory. >>>>>>>>> This simple
>>>>>>>>> exercise is just to confirm that it runs through correctly
>>>>>>>>> and the
>>>>>>>>> process finishes. The next thing to try is to repeat the
>>>>>>>>> above data
>>>>>>>>> structure but try the pepXML conversion in the GUI. >>>>>>>>> Hopefully this
>>>>>>>>> isolates whether you're experiencing a pepXML conversion
>>>>>>>>> problem or a
>>>>>>>>> GUI problem.
>>>>>>>>> - Jimmy
>>>>>>>>> Antonio wrote:
>>>>>>>>>> Hi Jimmy,
>>>>>>>>>> I run Sequest from Bioworks on our computer cluster, and then
>>>> transfer
>>>>>>>>>> the files to the local machine running TPP, so yeas I had
>>>>>>>>>> the c:/
>>>>>>>>>> Inetpub/wwwroot/ISB/data/AAS/test/
>>>>>>>>>> With the out-and dta- files in it.
>>>>>>>>>> I have attempted to run Sequest from TPP and I had the same
>>>>>>>>>> problem;
>>>>>>>>>> the dta and out files are created, but the command
>>>>>>>>>> indicates that is
>>>>>>>>>> still running. The problem occurs whether I send a few
>>>>>>>>>> files or a
>>>>>>>>>> single one. But I have more than one file on the queue, the
>>>>>>>>>> command
>>>>>>>>>> will not proceed to the next file. I can run Sequest from
>>>>>>>>>> Bioworks on
>>>>>>>>>> the local machine without any problems.
>>>>>>>>>> On Jul 2, 6:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote:
>>>>>>>>>>> Antonio,
>>>>>>>>>>> That warning about not being able to open the mzXML file
>>>>>>>>>>> is not
>>>>>>>>>>> indicative of the underlying problem. It is truly just a
>>>>>>>>>>> warning
>>>> and
>>>>>>>>>>> the analysis process is capable of finishing correctly
>>>>>>>>>>> even if the
>>>>>>>>>>> corresponding mzXML file is missing.
>>>>>>>>>>> The important question that's not clear from your
>>>>>>>>>>> description below
>>>> is
>>>>>>>>>>> how did you run the Sequest search? Did you run it
>>>>>>>>>>> separately via
>>>>>>>>>>> Bioworks or did you run the search through the TPP? >>>>>>>>>>> Although
>>>> helpful
>>>>>>>>>>> but not required, it doesn't seem like you did the
>>>>>>>>>>> latter. Do you
>>>> have
>>>>>>>>>>> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/)
>>>>>>>>>>> that has
>>>> the
>>>>>>>>>>> Sequest .out files in it?
>>>>>>>>>>> - Jimmy
>>>>>>>>>>> Antonio wrote:
>>>>>>>>>>>> I have installed TPP v4.2 on windows XP. I have created
>>>>>>>>>>>> the mzXML
>>>>>>>>>>>> datafiles from my Sequest search. Now I'm making the
>>>>>>>>>>>> corresponding
>>>>>>>>>>>> pepXML files. I see that the first file is being created,
>>>>>>>>>>>> it seems
>>>>>>>>>>>> that is finished but I see the following warming message
>>>>>>>>>>>> at the end
>>>> of
>>>>>>>>>>>> the "Output so far" field:
>>>>>>>>>>>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/ >>>>>>>>>>>> data/AAS/
>>>>>>>>>>>> test.mzXML" for reading MS instrument info and scan times.
>>>>>>>>>>>> And the command status window indicates that the command
>>>>>>>>>>>> is still
>>>>>>>>>>>> running. Is it? I do not see the file increasing in size.
>>>>>>>>>>>> I can
>>>> open
>>>>>>>>>>>> the pepxml file, although IE indicates that there is an
>>>>>>>>>>>> error on
>>>> page.
>>>>>>>>>>>> It seems to me that the program is stuck and is not
>>>>>>>>>>>> progressing to
>>>>>>>>>>>> next task: the creation of the next pepXML file. Solutions?
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Antonio- Hide quoted text -
>>>>>>>>>>> - Show quoted text -- Hide quoted text -
>>>>>>>>> - Show quoted text -- Hide quoted text -
>>>>>>> - Show quoted text -- Hide quoted text -
>>>>>> - Show quoted text -
|
