Re: [spctools-discuss] Comet search performance issue

2016-03-22 Thread bx2016uis 
Hi Luis,

You were correct on the poor data quality. I ran another data set and it 
was okay. Thanks for your insight.

Thanks again to Jimmy, Brian and Mike for your replies. Much appreciated.

With gratitude,

Bob

On Tuesday, March 22, 2016 at 3:03:56 PM UTC-4, Luis wrote:
>
> Very likely bad data (or bad analysis), since there are very few spectra:
>
> " read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra."
>
> The modeling fails after that (see the warnings) which means that likely 
> no data were written to an output file.  Check your search results first.
>
> Cheers,
> --Luis
>
>
>
> On Tue, Mar 22, 2016 at 11:59 AM, Jimmy Eng  > wrote:
>
>> Now that I look back, I could be interpreting the whole thing wrong.  The 
>> "\mydata (Comet)" might be completely normal and not meaning to reflect a 
>> directory path but rather simply indicate that it's a Comet search.  
>> Anyways, I don't use the Windows GUI much so I'm not the right person to 
>> help you here beyond noting that it is complaining about a path problem.
>>
>> On Tue, Mar 22, 2016 at 11:53 AM, > 
>> wrote:
>>
>>> Hi Jimmy,
>>>
>>> I used the GUI (http://localhost/tpp-bin/tpp_gui.pl) to do what I did. 
>>> The "\data (Comet)" part was spit out by the system. I was also puzzled by 
>>> that myself. I clearly selected the input file (mydata.pep.xml) from a 
>>> valid folder. I am going to try to do it from the command line using the 
>>> "cheat" method that Brian suggested earlier.
>>>
>>> Thanks,
>>>
>>> Bob
>>>
>>> On Tuesday, March 22, 2016 at 2:40:15 PM UTC-4, Jimmy Eng wrote:

 The error is that "The system cannot find the path specified" which 
 appears to be "c:\Inetpub\wwwroot\ISB\data\mydata\mydata (Comet)\".  If 
 that is the problem, get rid of the space in the directory path "\data 
 (Comet)".  You should get in the habit of also not including any special 
 characters (like the parenthesis) in the path or the file names.  If you 
 just stick with letters, numbers, dashes "-", and underscores "_" then you 
 won't have issues later.

 So rename the directory and try again.

 - Jimmy

 On Tue, Mar 22, 2016 at 11:18 AM,  wrote:

> Hi Jimmy,
>
> I updated comet.exe and comet.params (I grabbed comet.params.high-high 
> because mydata was from QExactive). The database search itself seemed to 
> have worked. But when I did Analyze Peptides, an error occurred. Please 
> see 
> the message below. Could you please take a look?
>
> Thanks,
>
> Bob
>
> c:\Inetpub\tpp-bin\xinteract (TPP v4.8.0 PHILAE, Build 201411201551-6764 
> (mingw-i686))
>  PPM mode in Accurate Mass Model ...
>
> running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" 
> "mydata.pep.xml" -L"7""
>  file 1: mydata.pep.xml
> SUCCESS: CORRECTED data file 
> c:\Inetpub\wwwroot\ISB\data\mydata\mydata.mzXML in msms_run_summary tag 
> ...
>  processed altogether 664 results
> INFO: Results written to file: 
> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml
> command completed in 1 sec 
>
> running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml""
> command completed in 0 sec 
>
> running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" 
> "c:/Inetpub/wwwroot/ISB/data/dbase/speclibs/human_uniprot_sprot.fasta""
>   - Searching the tree...
>   - Linking duplicate entries...  - Printing results...
>
>   - Building Commentz-Walter keyword tree...command completed in 3 sec 
>
> running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" 
> MINPROB=0.05 PPM"
> using PPM mass difference
>  (Comet)
> init with Comet trypsin 
> MS Instrument info: Manufacturer: Thermo Scientific, Model: Q Exactive, 
> Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
>
>  PeptideProphet  (TPP v4.8.0 PHILAE, Build 201411201551-6764 
> (mingw-i686)) AKeller@ISB
>  read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
> Initialising statistical models ...
> Iterations: .10.20.WARNING: Mixture model quality test 
> failed for charge (1+).WARNING: Mixture model quality test failed for 
> charge (2+).WARNING: Mixture model quality test failed for charge (3+).
> model complete after 22 iterations
> command completed in 0 sec 
>
> running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml"
> Analyzing interact.pep.xml ...
> Parsing search results "c:\Inetpub\wwwroot\ISB\data\mydata\mydata 
> (Comet)"...
>   => Found 0 hits. (0 decoys, 0 excluded)
>   => Total so far: 0 hits. (0 decoys, 0 excluded)
> The system cannot find the path specified.
> command completed in 0 sec 
>
> running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml"
>
> command "

Re: [spctools-discuss] Comet search performance issue

2016-03-22 Thread Luis Mendoza 
As of the previous couple of releases, the default is to use the parameters
directory as the output location for Comet searches.  This is to make it
easier to manage multiple searches of the same data and avoid overwriting
files.  Ideally, the comet.params would first get copied to the target
directory and edited before starting the search.

In this case I have the feeling that the wrong database is being used,
though I know nothing about the data.

Cheers,
--Luis


On Tue, Mar 22, 2016 at 12:15 PM, Jimmy Eng  wrote:

> A related weird part is that it looks like it's looking for (and
> presumably writing) the output here:
>
>c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml
>
> even though the input data was in
>
>c:\Inetpub\wwwroot\ISB\data\mydata\
>
>
> On Tue, Mar 22, 2016 at 12:03 PM, Luis Mendoza <
> luis.mend...@systemsbiology.org> wrote:
>
>> Very likely bad data (or bad analysis), since there are very few spectra:
>>
>> " read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra."
>>
>> The modeling fails after that (see the warnings) which means that likely
>> no data were written to an output file.  Check your search results first.
>>
>> Cheers,
>> --Luis
>>
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Re: [spctools-discuss] Comet search performance issue

2016-03-22 Thread Jimmy Eng 
A related weird part is that it looks like it's looking for (and presumably
writing) the output here:

   c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml

even though the input data was in

   c:\Inetpub\wwwroot\ISB\data\mydata\


On Tue, Mar 22, 2016 at 12:03 PM, Luis Mendoza <
luis.mend...@systemsbiology.org> wrote:

> Very likely bad data (or bad analysis), since there are very few spectra:
>
> " read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra."
>
> The modeling fails after that (see the warnings) which means that likely
> no data were written to an output file.  Check your search results first.
>
> Cheers,
> --Luis
>

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Re: [spctools-discuss] Comet search performance issue

2016-03-22 Thread Luis Mendoza 
Very likely bad data (or bad analysis), since there are very few spectra:

" read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra."

The modeling fails after that (see the warnings) which means that likely no
data were written to an output file.  Check your search results first.

Cheers,
--Luis



On Tue, Mar 22, 2016 at 11:59 AM, Jimmy Eng  wrote:

> Now that I look back, I could be interpreting the whole thing wrong.  The
> "\mydata (Comet)" might be completely normal and not meaning to reflect a
> directory path but rather simply indicate that it's a Comet search.
> Anyways, I don't use the Windows GUI much so I'm not the right person to
> help you here beyond noting that it is complaining about a path problem.
>
> On Tue, Mar 22, 2016 at 11:53 AM,  wrote:
>
>> Hi Jimmy,
>>
>> I used the GUI (http://localhost/tpp-bin/tpp_gui.pl) to do what I did.
>> The "\data (Comet)" part was spit out by the system. I was also puzzled by
>> that myself. I clearly selected the input file (mydata.pep.xml) from a
>> valid folder. I am going to try to do it from the command line using the
>> "cheat" method that Brian suggested earlier.
>>
>> Thanks,
>>
>> Bob
>>
>> On Tuesday, March 22, 2016 at 2:40:15 PM UTC-4, Jimmy Eng wrote:
>>>
>>> The error is that "The system cannot find the path specified" which
>>> appears to be "c:\Inetpub\wwwroot\ISB\data\mydata\mydata (Comet)\".  If
>>> that is the problem, get rid of the space in the directory path "\data
>>> (Comet)".  You should get in the habit of also not including any special
>>> characters (like the parenthesis) in the path or the file names.  If you
>>> just stick with letters, numbers, dashes "-", and underscores "_" then you
>>> won't have issues later.
>>>
>>> So rename the directory and try again.
>>>
>>> - Jimmy
>>>
>>> On Tue, Mar 22, 2016 at 11:18 AM,  wrote:
>>>
 Hi Jimmy,

 I updated comet.exe and comet.params (I grabbed comet.params.high-high
 because mydata was from QExactive). The database search itself seemed to
 have worked. But when I did Analyze Peptides, an error occurred. Please see
 the message below. Could you please take a look?

 Thanks,

 Bob

 c:\Inetpub\tpp-bin\xinteract (TPP v4.8.0 PHILAE, Build 201411201551-6764 
 (mingw-i686))
  PPM mode in Accurate Mass Model ...

 running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" 
 "mydata.pep.xml" -L"7""
  file 1: mydata.pep.xml
 SUCCESS: CORRECTED data file 
 c:\Inetpub\wwwroot\ISB\data\mydata\mydata.mzXML in msms_run_summary tag ...
  processed altogether 664 results
 INFO: Results written to file: 
 c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml
 command completed in 1 sec

 running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml""
 command completed in 0 sec

 running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" 
 "c:/Inetpub/wwwroot/ISB/data/dbase/speclibs/human_uniprot_sprot.fasta""
   - Searching the tree...
   - Linking duplicate entries...  - Printing results...

   - Building Commentz-Walter keyword tree...command completed in 3 sec

 running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" 
 MINPROB=0.05 PPM"
 using PPM mass difference
  (Comet)
 init with Comet trypsin
 MS Instrument info: Manufacturer: Thermo Scientific, Model: Q Exactive, 
 Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

  PeptideProphet  (TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686)) 
 AKeller@ISB
  read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
 Initialising statistical models ...
 Iterations: .10.20.WARNING: Mixture model quality test 
 failed for charge (1+).WARNING: Mixture model quality test failed for 
 charge (2+).WARNING: Mixture model quality test failed for charge (3+).
 model complete after 22 iterations
 command completed in 0 sec

 running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml"
 Analyzing interact.pep.xml ...
 Parsing search results "c:\Inetpub\wwwroot\ISB\data\mydata\mydata 
 (Comet)"...
   => Found 0 hits. (0 decoys, 0 excluded)
   => Total so far: 0 hits. (0 decoys, 0 excluded)
 The system cannot find the path specified.
 command completed in 0 sec

 running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
 c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml"

 command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
 c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" failed: Unknown 
 error

 command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
 c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" exited with 
 non-zero exit code: 255
 QUIT - the job is incomplete


 *Command FAILED*
 RETURN CODE:65280


 On Tuesday, March 22, 2016 at

Re: [spctools-discuss] Comet search performance issue

2016-03-22 Thread Jimmy Eng 
Now that I look back, I could be interpreting the whole thing wrong.  The
"\mydata (Comet)" might be completely normal and not meaning to reflect a
directory path but rather simply indicate that it's a Comet search.
Anyways, I don't use the Windows GUI much so I'm not the right person to
help you here beyond noting that it is complaining about a path problem.

On Tue, Mar 22, 2016 at 11:53 AM,  wrote:

> Hi Jimmy,
>
> I used the GUI (http://localhost/tpp-bin/tpp_gui.pl) to do what I did.
> The "\data (Comet)" part was spit out by the system. I was also puzzled by
> that myself. I clearly selected the input file (mydata.pep.xml) from a
> valid folder. I am going to try to do it from the command line using the
> "cheat" method that Brian suggested earlier.
>
> Thanks,
>
> Bob
>
> On Tuesday, March 22, 2016 at 2:40:15 PM UTC-4, Jimmy Eng wrote:
>>
>> The error is that "The system cannot find the path specified" which
>> appears to be "c:\Inetpub\wwwroot\ISB\data\mydata\mydata (Comet)\".  If
>> that is the problem, get rid of the space in the directory path "\data
>> (Comet)".  You should get in the habit of also not including any special
>> characters (like the parenthesis) in the path or the file names.  If you
>> just stick with letters, numbers, dashes "-", and underscores "_" then you
>> won't have issues later.
>>
>> So rename the directory and try again.
>>
>> - Jimmy
>>
>> On Tue, Mar 22, 2016 at 11:18 AM,  wrote:
>>
>>> Hi Jimmy,
>>>
>>> I updated comet.exe and comet.params (I grabbed comet.params.high-high
>>> because mydata was from QExactive). The database search itself seemed to
>>> have worked. But when I did Analyze Peptides, an error occurred. Please see
>>> the message below. Could you please take a look?
>>>
>>> Thanks,
>>>
>>> Bob
>>>
>>> c:\Inetpub\tpp-bin\xinteract (TPP v4.8.0 PHILAE, Build 201411201551-6764 
>>> (mingw-i686))
>>>  PPM mode in Accurate Mass Model ...
>>>
>>> running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" 
>>> "mydata.pep.xml" -L"7""
>>>  file 1: mydata.pep.xml
>>> SUCCESS: CORRECTED data file 
>>> c:\Inetpub\wwwroot\ISB\data\mydata\mydata.mzXML in msms_run_summary tag ...
>>>  processed altogether 664 results
>>> INFO: Results written to file: 
>>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml
>>> command completed in 1 sec
>>>
>>> running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml""
>>> command completed in 0 sec
>>>
>>> running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" 
>>> "c:/Inetpub/wwwroot/ISB/data/dbase/speclibs/human_uniprot_sprot.fasta""
>>>   - Searching the tree...
>>>   - Linking duplicate entries...  - Printing results...
>>>
>>>   - Building Commentz-Walter keyword tree...command completed in 3 sec
>>>
>>> running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" 
>>> MINPROB=0.05 PPM"
>>> using PPM mass difference
>>>  (Comet)
>>> init with Comet trypsin
>>> MS Instrument info: Manufacturer: Thermo Scientific, Model: Q Exactive, 
>>> Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
>>>
>>>  PeptideProphet  (TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686)) 
>>> AKeller@ISB
>>>  read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
>>> Initialising statistical models ...
>>> Iterations: .10.20.WARNING: Mixture model quality test 
>>> failed for charge (1+).WARNING: Mixture model quality test failed for 
>>> charge (2+).WARNING: Mixture model quality test failed for charge (3+).
>>> model complete after 22 iterations
>>> command completed in 0 sec
>>>
>>> running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml"
>>> Analyzing interact.pep.xml ...
>>> Parsing search results "c:\Inetpub\wwwroot\ISB\data\mydata\mydata 
>>> (Comet)"...
>>>   => Found 0 hits. (0 decoys, 0 excluded)
>>>   => Total so far: 0 hits. (0 decoys, 0 excluded)
>>> The system cannot find the path specified.
>>> command completed in 0 sec
>>>
>>> running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
>>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml"
>>>
>>> command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
>>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" failed: Unknown 
>>> error
>>>
>>> command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
>>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" exited with 
>>> non-zero exit code: 255
>>> QUIT - the job is incomplete
>>>
>>>
>>> *Command FAILED*
>>> RETURN CODE:65280
>>>
>>>
>>> On Tuesday, March 22, 2016 at 11:49:23 AM UTC-4, Jimmy Eng wrote:

 Besides using a very old version of Comet, there's nothing wrong with
 the parameter settings that would indicate why you might see an extremely
 long search.  As Brian and Mike suggested, it's likely Comet's not even
 running right now for whatever reason.

 You're using version 2014.02 rev. 2 that was released in September
 2014.  Before doing anything else, it's in your best interest to update to
 the l

Re: [spctools-discuss] Comet search performance issue

2016-03-22 Thread bx2016uis 
Hi Jimmy,

I used the GUI (http://localhost/tpp-bin/tpp_gui.pl) to do what I did. The 
"\data (Comet)" part was spit out by the system. I was also puzzled by that 
myself. I clearly selected the input file (mydata.pep.xml) from a valid 
folder. I am going to try to do it from the command line using the "cheat" 
method that Brian suggested earlier.

Thanks,

Bob

On Tuesday, March 22, 2016 at 2:40:15 PM UTC-4, Jimmy Eng wrote:
>
> The error is that "The system cannot find the path specified" which 
> appears to be "c:\Inetpub\wwwroot\ISB\data\mydata\mydata (Comet)\".  If 
> that is the problem, get rid of the space in the directory path "\data 
> (Comet)".  You should get in the habit of also not including any special 
> characters (like the parenthesis) in the path or the file names.  If you 
> just stick with letters, numbers, dashes "-", and underscores "_" then you 
> won't have issues later.
>
> So rename the directory and try again.
>
> - Jimmy
>
> On Tue, Mar 22, 2016 at 11:18 AM, > wrote:
>
>> Hi Jimmy,
>>
>> I updated comet.exe and comet.params (I grabbed comet.params.high-high 
>> because mydata was from QExactive). The database search itself seemed to 
>> have worked. But when I did Analyze Peptides, an error occurred. Please see 
>> the message below. Could you please take a look?
>>
>> Thanks,
>>
>> Bob
>>
>> c:\Inetpub\tpp-bin\xinteract (TPP v4.8.0 PHILAE, Build 201411201551-6764 
>> (mingw-i686))
>>  PPM mode in Accurate Mass Model ...
>>
>> running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" 
>> "mydata.pep.xml" -L"7""
>>  file 1: mydata.pep.xml
>> SUCCESS: CORRECTED data file c:\Inetpub\wwwroot\ISB\data\mydata\mydata.mzXML 
>> in msms_run_summary tag ...
>>  processed altogether 664 results
>> INFO: Results written to file: 
>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml
>> command completed in 1 sec 
>>
>> running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml""
>> command completed in 0 sec 
>>
>> running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" 
>> "c:/Inetpub/wwwroot/ISB/data/dbase/speclibs/human_uniprot_sprot.fasta""
>>   - Searching the tree...
>>   - Linking duplicate entries...  - Printing results...
>>
>>   - Building Commentz-Walter keyword tree...command completed in 3 sec 
>>
>> running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" 
>> MINPROB=0.05 PPM"
>> using PPM mass difference
>>  (Comet)
>> init with Comet trypsin 
>> MS Instrument info: Manufacturer: Thermo Scientific, Model: Q Exactive, 
>> Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
>>
>>  PeptideProphet  (TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686)) 
>> AKeller@ISB
>>  read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
>> Initialising statistical models ...
>> Iterations: .10.20.WARNING: Mixture model quality test 
>> failed for charge (1+).WARNING: Mixture model quality test failed for charge 
>> (2+).WARNING: Mixture model quality test failed for charge (3+).
>> model complete after 22 iterations
>> command completed in 0 sec 
>>
>> running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml"
>> Analyzing interact.pep.xml ...
>> Parsing search results "c:\Inetpub\wwwroot\ISB\data\mydata\mydata (Comet)"...
>>   => Found 0 hits. (0 decoys, 0 excluded)
>>   => Total so far: 0 hits. (0 decoys, 0 excluded)
>> The system cannot find the path specified.
>> command completed in 0 sec 
>>
>> running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml"
>>
>> command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" failed: Unknown 
>> error
>>
>> command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" exited with 
>> non-zero exit code: 255
>> QUIT - the job is incomplete
>>
>>
>> *Command FAILED*
>> RETURN CODE:65280
>>
>>
>> On Tuesday, March 22, 2016 at 11:49:23 AM UTC-4, Jimmy Eng wrote:
>>>
>>> Besides using a very old version of Comet, there's nothing wrong with 
>>> the parameter settings that would indicate why you might see an extremely 
>>> long search.  As Brian and Mike suggested, it's likely Comet's not even 
>>> running right now for whatever reason.
>>>
>>> You're using version 2014.02 rev. 2 that was released in September 
>>> 2014.  Before doing anything else, it's in your best interest to update to 
>>> the latest 2016.01 rev. 0 release that you can download from here:
>>>
>>>https://sourceforge.net/projects/comet-ms/files/
>>>
>>> Grab the file comet_binaries_2016010.zip.  Find your current Comet 
>>> binary (should be at c:\inetpub\tpp-bin\comet.exe) and replace it with the 
>>> binary in this zip file (rename comet.2016010.win64.exe to 
>>> c:\inetpub\tpp-bin\comet.exe).  Then generate a new comet.params file or 
>>> grab the comet.params.low-low 
>>>

Re: [spctools-discuss] Comet search performance issue

2016-03-22 Thread Jimmy Eng 
The error is that "The system cannot find the path specified" which appears
to be "c:\Inetpub\wwwroot\ISB\data\mydata\mydata (Comet)\".  If that is the
problem, get rid of the space in the directory path "\data (Comet)".  You
should get in the habit of also not including any special characters (like
the parenthesis) in the path or the file names.  If you just stick with
letters, numbers, dashes "-", and underscores "_" then you won't have
issues later.

So rename the directory and try again.

- Jimmy

On Tue, Mar 22, 2016 at 11:18 AM,  wrote:

> Hi Jimmy,
>
> I updated comet.exe and comet.params (I grabbed comet.params.high-high
> because mydata was from QExactive). The database search itself seemed to
> have worked. But when I did Analyze Peptides, an error occurred. Please see
> the message below. Could you please take a look?
>
> Thanks,
>
> Bob
>
> c:\Inetpub\tpp-bin\xinteract (TPP v4.8.0 PHILAE, Build 201411201551-6764 
> (mingw-i686))
>  PPM mode in Accurate Mass Model ...
>
> running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" 
> "mydata.pep.xml" -L"7""
>  file 1: mydata.pep.xml
> SUCCESS: CORRECTED data file c:\Inetpub\wwwroot\ISB\data\mydata\mydata.mzXML 
> in msms_run_summary tag ...
>  processed altogether 664 results
> INFO: Results written to file: 
> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml
> command completed in 1 sec
>
> running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml""
> command completed in 0 sec
>
> running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" 
> "c:/Inetpub/wwwroot/ISB/data/dbase/speclibs/human_uniprot_sprot.fasta""
>   - Searching the tree...
>   - Linking duplicate entries...  - Printing results...
>
>   - Building Commentz-Walter keyword tree...command completed in 3 sec
>
> running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" 
> MINPROB=0.05 PPM"
> using PPM mass difference
>  (Comet)
> init with Comet trypsin
> MS Instrument info: Manufacturer: Thermo Scientific, Model: Q Exactive, 
> Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
>
>  PeptideProphet  (TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686)) 
> AKeller@ISB
>  read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
> Initialising statistical models ...
> Iterations: .10.20.WARNING: Mixture model quality test failed 
> for charge (1+).WARNING: Mixture model quality test failed for charge 
> (2+).WARNING: Mixture model quality test failed for charge (3+).
> model complete after 22 iterations
> command completed in 0 sec
>
> running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml"
> Analyzing interact.pep.xml ...
> Parsing search results "c:\Inetpub\wwwroot\ISB\data\mydata\mydata (Comet)"...
>   => Found 0 hits. (0 decoys, 0 excluded)
>   => Total so far: 0 hits. (0 decoys, 0 excluded)
> The system cannot find the path specified.
> command completed in 0 sec
>
> running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml"
>
> command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" failed: Unknown error
>
> command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" exited with non-zero 
> exit code: 255
> QUIT - the job is incomplete
>
>
> *Command FAILED*
> RETURN CODE:65280
>
>
> On Tuesday, March 22, 2016 at 11:49:23 AM UTC-4, Jimmy Eng wrote:
>>
>> Besides using a very old version of Comet, there's nothing wrong with the
>> parameter settings that would indicate why you might see an extremely long
>> search.  As Brian and Mike suggested, it's likely Comet's not even running
>> right now for whatever reason.
>>
>> You're using version 2014.02 rev. 2 that was released in September 2014.
>> Before doing anything else, it's in your best interest to update to the
>> latest 2016.01 rev. 0 release that you can download from here:
>>
>>https://sourceforge.net/projects/comet-ms/files/
>>
>> Grab the file comet_binaries_2016010.zip.  Find your current Comet binary
>> (should be at c:\inetpub\tpp-bin\comet.exe) and replace it with the binary
>> in this zip file (rename comet.2016010.win64.exe to
>> c:\inetpub\tpp-bin\comet.exe).  Then generate a new comet.params file or
>> grab the comet.params.low-low
>> 
>> from link below and rename to comet.params in the appropriate directory and
>> attempt a search again.
>>
>>http://comet-ms.sourceforge.net/parameters/parameters_201601/
>>
>> This search should complete in well under 10 minutes and not hours or
>> days.  Try the search again with the current Comet binary and report back
>> if you still have issues.
>>
>> - Jimmy
>>
>> On Tue, Mar 22, 2016 at 8:16 AM,  wrote:
>>
>>> Hi Jimmy, Brian and Mike,
>>>
>>> Thank you all for your replies. Please see below the content of my
>>> comet.params file (

Re: [spctools-discuss] Comet search performance issue

2016-03-22 Thread bx2016uis 
Hi Jimmy,

I updated comet.exe and comet.params (I grabbed comet.params.high-high 
because mydata was from QExactive). The database search itself seemed to 
have worked. But when I did Analyze Peptides, an error occurred. Please see 
the message below. Could you please take a look?

Thanks,

Bob

c:\Inetpub\tpp-bin\xinteract (TPP v4.8.0 PHILAE, Build 201411201551-6764 
(mingw-i686))
 PPM mode in Accurate Mass Model ...

running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "mydata.pep.xml" 
-L"7""
 file 1: mydata.pep.xml
SUCCESS: CORRECTED data file c:\Inetpub\wwwroot\ISB\data\mydata\mydata.mzXML in 
msms_run_summary tag ...
 processed altogether 664 results
INFO: Results written to file: 
c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml
command completed in 1 sec 

running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml""
command completed in 0 sec 

running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" 
"c:/Inetpub/wwwroot/ISB/data/dbase/speclibs/human_uniprot_sprot.fasta""
  - Searching the tree...
  - Linking duplicate entries...  - Printing results...

  - Building Commentz-Walter keyword tree...command completed in 3 sec 

running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" 
MINPROB=0.05 PPM"
using PPM mass difference
 (Comet)
init with Comet trypsin 
MS Instrument info: Manufacturer: Thermo Scientific, Model: Q Exactive, 
Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

 PeptideProphet  (TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686)) 
AKeller@ISB
 read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Iterations: .10.20.WARNING: Mixture model quality test failed 
for charge (1+).WARNING: Mixture model quality test failed for charge 
(2+).WARNING: Mixture model quality test failed for charge (3+).
model complete after 22 iterations
command completed in 0 sec 

running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml"
Analyzing interact.pep.xml ...
Parsing search results "c:\Inetpub\wwwroot\ISB\data\mydata\mydata (Comet)"...
  => Found 0 hits. (0 decoys, 0 excluded)
  => Total so far: 0 hits. (0 decoys, 0 excluded)
The system cannot find the path specified.
command completed in 0 sec 

running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml"

command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" failed: Unknown error

command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I 
c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" exited with non-zero 
exit code: 255
QUIT - the job is incomplete


*Command FAILED*
RETURN CODE:65280


On Tuesday, March 22, 2016 at 11:49:23 AM UTC-4, Jimmy Eng wrote:
>
> Besides using a very old version of Comet, there's nothing wrong with the 
> parameter settings that would indicate why you might see an extremely long 
> search.  As Brian and Mike suggested, it's likely Comet's not even running 
> right now for whatever reason.
>
> You're using version 2014.02 rev. 2 that was released in September 2014.  
> Before doing anything else, it's in your best interest to update to the 
> latest 2016.01 rev. 0 release that you can download from here:
>
>https://sourceforge.net/projects/comet-ms/files/
>
> Grab the file comet_binaries_2016010.zip.  Find your current Comet binary 
> (should be at c:\inetpub\tpp-bin\comet.exe) and replace it with the binary 
> in this zip file (rename comet.2016010.win64.exe to 
> c:\inetpub\tpp-bin\comet.exe).  Then generate a new comet.params file or 
> grab the comet.params.low-low 
> 
>  
> from link below and rename to comet.params in the appropriate directory and 
> attempt a search again.
>
>http://comet-ms.sourceforge.net/parameters/parameters_201601/
>
> This search should complete in well under 10 minutes and not hours or 
> days.  Try the search again with the current Comet binary and report back 
> if you still have issues.
>
> - Jimmy
>
> On Tue, Mar 22, 2016 at 8:16 AM, > wrote:
>
>> Hi Jimmy, Brian and Mike,
>>
>> Thank you all for your replies. Please see below the content of my 
>> comet.params file (again, this came with TPP installation, I did not modify 
>> it).
>>
>> Thanks,
>>
>> Bob
>>
>> # comet_version 2014.02 rev. 2
>> # Comet MS/MS search engine parameters file.
>> # Everything following the '#' symbol is treated as a comment.
>>
>> database_name = /some/path/db.fasta
>> decoy_search = 0   # 0=no (default), 1=concatenated 
>> search, 2=separate search
>>
>> num_threads = 0# 0=poll CPU to set num threads; 
>> else specify num threads directly (max 64)
>>
>> #
>> # masses
>> #
>> peptide_mass_tolerance = 3.00
>> peptide_mass_units = 0 # 0=amu, 1=mmu, 2=ppm
>> mass_type_parent = 1   # 0=average masse

Re: [spctools-discuss] Comet search performance issue

2016-03-22 Thread bx2016uis 
Thank you, Jimmy. I'll try what you suggested. -Bob

On Tuesday, March 22, 2016 at 11:49:23 AM UTC-4, Jimmy Eng wrote:
>
> Besides using a very old version of Comet, there's nothing wrong with the 
> parameter settings that would indicate why you might see an extremely long 
> search.  As Brian and Mike suggested, it's likely Comet's not even running 
> right now for whatever reason.
>
> You're using version 2014.02 rev. 2 that was released in September 2014.  
> Before doing anything else, it's in your best interest to update to the 
> latest 2016.01 rev. 0 release that you can download from here:
>
>https://sourceforge.net/projects/comet-ms/files/
>
> Grab the file comet_binaries_2016010.zip.  Find your current Comet binary 
> (should be at c:\inetpub\tpp-bin\comet.exe) and replace it with the binary 
> in this zip file (rename comet.2016010.win64.exe to 
> c:\inetpub\tpp-bin\comet.exe).  Then generate a new comet.params file or 
> grab the comet.params.low-low 
> 
>  
> from link below and rename to comet.params in the appropriate directory and 
> attempt a search again.
>
>http://comet-ms.sourceforge.net/parameters/parameters_201601/
>
> This search should complete in well under 10 minutes and not hours or 
> days.  Try the search again with the current Comet binary and report back 
> if you still have issues.
>
> - Jimmy
>
> On Tue, Mar 22, 2016 at 8:16 AM, > wrote:
>
>> Hi Jimmy, Brian and Mike,
>>
>> Thank you all for your replies. Please see below the content of my 
>> comet.params file (again, this came with TPP installation, I did not modify 
>> it).
>>
>> Thanks,
>>
>> Bob
>>
>> # comet_version 2014.02 rev. 2
>> # Comet MS/MS search engine parameters file.
>> # Everything following the '#' symbol is treated as a comment.
>>
>> database_name = /some/path/db.fasta
>> decoy_search = 0   # 0=no (default), 1=concatenated 
>> search, 2=separate search
>>
>> num_threads = 0# 0=poll CPU to set num threads; 
>> else specify num threads directly (max 64)
>>
>> #
>> # masses
>> #
>> peptide_mass_tolerance = 3.00
>> peptide_mass_units = 0 # 0=amu, 1=mmu, 2=ppm
>> mass_type_parent = 1   # 0=average masses, 1=monoisotopic 
>> masses
>> mass_type_fragment = 1 # 0=average masses, 1=monoisotopic 
>> masses
>> isotope_error = 0  # 0=off, 1=on -1/0/1/2/3 (standard 
>> C13 error), 2= -8/-4/0/4/8 (for +4/+8 labeling)
>>
>> #
>> # search enzyme
>> #
>> search_enzyme_number = 1   # choose from list at end of this 
>> params file
>> num_enzyme_termini = 2 # valid values are 1 
>> (semi-digested), 2 (fully digested, default), 8 N-term, 9 C-term
>> allowed_missed_cleavage = 2# maximum value is 5; for enzyme 
>> search
>>
>> #
>> # Up to 9 variable modifications are supported
>> # format:<0=variable/1=binary>  
>>  
>> # e.g. 79.966331 STY 0 3 -1 0
>> #
>> variable_mod01 = 15.9949 M 0 3 -1 0
>> variable_mod02 = 0.0 X 0 3 -1 0
>> variable_mod03 = 0.0 X 0 3 -1 0
>> variable_mod04 = 0.0 X 0 3 -1 0
>> variable_mod05 = 0.0 X 0 3 -1 0
>> variable_mod06 = 0.0 X 0 3 -1 0
>> variable_mod07 = 0.0 X 0 3 -1 0
>> variable_mod08 = 0.0 X 0 3 -1 0
>> variable_mod09 = 0.0 X 0 3 -1 0
>> max_variable_mods_in_peptide = 5
>>
>> #
>> # fragment ions
>> #
>> # ion trap ms/ms:  1.0005 tolerance, 0.4 offset (mono masses), 
>> theoretical_fragment_ions = 1
>> # high res ms/ms:0.02 tolerance, 0.0 offset (mono masses), 
>> theoretical_fragment_ions = 0
>> #
>> fragment_bin_tol = 1.0005  # binning to use on fragment ions
>> fragment_bin_offset = 0.4  # offset position to start the 
>> binning (0.0 to 1.0)
>> theoretical_fragment_ions = 1  # 0=use flanking peaks, 1=M peak 
>> only
>> use_A_ions = 0
>> use_B_ions = 1
>> use_C_ions = 0
>> use_X_ions = 0
>> use_Y_ions = 1
>> use_Z_ions = 0
>> use_NL_ions = 1# 0=no, 1=yes to consider NH3/H2O 
>> neutral loss peaks
>> use_sparse_matrix = 0
>>
>> #
>> # output
>> #
>> output_sqtstream = 0   # 0=no, 1=yes  write sqt to 
>> standard output
>> output_sqtfile = 0 # 0=no, 1=yes  write sqt file
>> output_txtfile = 0 # 0=no, 1=yes  write tab-delimited 
>> txt file
>> output_pepxmlfile = 1  # 0=no, 1=yes  write pep.xml file
>> output_percolatorfile = 0  # 0=no, 1=yes  write Percolator 
>> tab-delimited input file
>> output_outfiles = 0# 0=no, 1=yes  write .out files
>> print_expect_score = 1 # 0=no, 1=yes to replace Sp with 
>> expect in out & sqt
>> num_output_lines = 5   # num peptide results to show
>> show_fragment_ions = 0 # 0=no, 1=yes for out files only
>>
>> sample_enzyme_number = 1   # Sample enzyme which is possibly 
>> different than the

Re: [spctools-discuss] Comet search performance issue

2016-03-22 Thread Jimmy Eng 
Besides using a very old version of Comet, there's nothing wrong with the
parameter settings that would indicate why you might see an extremely long
search.  As Brian and Mike suggested, it's likely Comet's not even running
right now for whatever reason.

You're using version 2014.02 rev. 2 that was released in September 2014.
Before doing anything else, it's in your best interest to update to the
latest 2016.01 rev. 0 release that you can download from here:

   https://sourceforge.net/projects/comet-ms/files/

Grab the file comet_binaries_2016010.zip.  Find your current Comet binary
(should be at c:\inetpub\tpp-bin\comet.exe) and replace it with the binary
in this zip file (rename comet.2016010.win64.exe to
c:\inetpub\tpp-bin\comet.exe).  Then generate a new comet.params file or
grab the comet.params.low-low

from link below and rename to comet.params in the appropriate directory and
attempt a search again.

   http://comet-ms.sourceforge.net/parameters/parameters_201601/

This search should complete in well under 10 minutes and not hours or
days.  Try the search again with the current Comet binary and report back
if you still have issues.

- Jimmy

On Tue, Mar 22, 2016 at 8:16 AM,  wrote:

> Hi Jimmy, Brian and Mike,
>
> Thank you all for your replies. Please see below the content of my
> comet.params file (again, this came with TPP installation, I did not modify
> it).
>
> Thanks,
>
> Bob
>
> # comet_version 2014.02 rev. 2
> # Comet MS/MS search engine parameters file.
> # Everything following the '#' symbol is treated as a comment.
>
> database_name = /some/path/db.fasta
> decoy_search = 0   # 0=no (default), 1=concatenated
> search, 2=separate search
>
> num_threads = 0# 0=poll CPU to set num threads;
> else specify num threads directly (max 64)
>
> #
> # masses
> #
> peptide_mass_tolerance = 3.00
> peptide_mass_units = 0 # 0=amu, 1=mmu, 2=ppm
> mass_type_parent = 1   # 0=average masses, 1=monoisotopic
> masses
> mass_type_fragment = 1 # 0=average masses, 1=monoisotopic
> masses
> isotope_error = 0  # 0=off, 1=on -1/0/1/2/3 (standard
> C13 error), 2= -8/-4/0/4/8 (for +4/+8 labeling)
>
> #
> # search enzyme
> #
> search_enzyme_number = 1   # choose from list at end of this
> params file
> num_enzyme_termini = 2 # valid values are 1
> (semi-digested), 2 (fully digested, default), 8 N-term, 9 C-term
> allowed_missed_cleavage = 2# maximum value is 5; for enzyme
> search
>
> #
> # Up to 9 variable modifications are supported
> # format:<0=variable/1=binary> 
>  
> # e.g. 79.966331 STY 0 3 -1 0
> #
> variable_mod01 = 15.9949 M 0 3 -1 0
> variable_mod02 = 0.0 X 0 3 -1 0
> variable_mod03 = 0.0 X 0 3 -1 0
> variable_mod04 = 0.0 X 0 3 -1 0
> variable_mod05 = 0.0 X 0 3 -1 0
> variable_mod06 = 0.0 X 0 3 -1 0
> variable_mod07 = 0.0 X 0 3 -1 0
> variable_mod08 = 0.0 X 0 3 -1 0
> variable_mod09 = 0.0 X 0 3 -1 0
> max_variable_mods_in_peptide = 5
>
> #
> # fragment ions
> #
> # ion trap ms/ms:  1.0005 tolerance, 0.4 offset (mono masses),
> theoretical_fragment_ions = 1
> # high res ms/ms:0.02 tolerance, 0.0 offset (mono masses),
> theoretical_fragment_ions = 0
> #
> fragment_bin_tol = 1.0005  # binning to use on fragment ions
> fragment_bin_offset = 0.4  # offset position to start the
> binning (0.0 to 1.0)
> theoretical_fragment_ions = 1  # 0=use flanking peaks, 1=M peak
> only
> use_A_ions = 0
> use_B_ions = 1
> use_C_ions = 0
> use_X_ions = 0
> use_Y_ions = 1
> use_Z_ions = 0
> use_NL_ions = 1# 0=no, 1=yes to consider NH3/H2O
> neutral loss peaks
> use_sparse_matrix = 0
>
> #
> # output
> #
> output_sqtstream = 0   # 0=no, 1=yes  write sqt to
> standard output
> output_sqtfile = 0 # 0=no, 1=yes  write sqt file
> output_txtfile = 0 # 0=no, 1=yes  write tab-delimited
> txt file
> output_pepxmlfile = 1  # 0=no, 1=yes  write pep.xml file
> output_percolatorfile = 0  # 0=no, 1=yes  write Percolator
> tab-delimited input file
> output_outfiles = 0# 0=no, 1=yes  write .out files
> print_expect_score = 1 # 0=no, 1=yes to replace Sp with
> expect in out & sqt
> num_output_lines = 5   # num peptide results to show
> show_fragment_ions = 0 # 0=no, 1=yes for out files only
>
> sample_enzyme_number = 1   # Sample enzyme which is possibly
> different than the one applied to the search.
># Used to calculate NTT & NMC in
> pepXML output (default=1 for trypsin).
>
> #
> # mzXML parameters
> #
> scan_range = 0 0   # start and scan scan range to
> search; 0 as 1st entry ignores parameter
> precursor_charge = 0 0

Re: [spctools-discuss] Comet search performance issue

2016-03-22 Thread bx2016uis 
Hi Jimmy, Brian and Mike,

Thank you all for your replies. Please see below the content of my 
comet.params file (again, this came with TPP installation, I did not modify 
it).

Thanks,

Bob

# comet_version 2014.02 rev. 2
# Comet MS/MS search engine parameters file.
# Everything following the '#' symbol is treated as a comment.

database_name = /some/path/db.fasta
decoy_search = 0   # 0=no (default), 1=concatenated 
search, 2=separate search

num_threads = 0# 0=poll CPU to set num threads; 
else specify num threads directly (max 64)

#
# masses
#
peptide_mass_tolerance = 3.00
peptide_mass_units = 0 # 0=amu, 1=mmu, 2=ppm
mass_type_parent = 1   # 0=average masses, 1=monoisotopic 
masses
mass_type_fragment = 1 # 0=average masses, 1=monoisotopic 
masses
isotope_error = 0  # 0=off, 1=on -1/0/1/2/3 (standard 
C13 error), 2= -8/-4/0/4/8 (for +4/+8 labeling)

#
# search enzyme
#
search_enzyme_number = 1   # choose from list at end of this 
params file
num_enzyme_termini = 2 # valid values are 1 
(semi-digested), 2 (fully digested, default), 8 N-term, 9 C-term
allowed_missed_cleavage = 2# maximum value is 5; for enzyme 
search

#
# Up to 9 variable modifications are supported
# format:<0=variable/1=binary>  
 
# e.g. 79.966331 STY 0 3 -1 0
#
variable_mod01 = 15.9949 M 0 3 -1 0
variable_mod02 = 0.0 X 0 3 -1 0
variable_mod03 = 0.0 X 0 3 -1 0
variable_mod04 = 0.0 X 0 3 -1 0
variable_mod05 = 0.0 X 0 3 -1 0
variable_mod06 = 0.0 X 0 3 -1 0
variable_mod07 = 0.0 X 0 3 -1 0
variable_mod08 = 0.0 X 0 3 -1 0
variable_mod09 = 0.0 X 0 3 -1 0
max_variable_mods_in_peptide = 5

#
# fragment ions
#
# ion trap ms/ms:  1.0005 tolerance, 0.4 offset (mono masses), 
theoretical_fragment_ions = 1
# high res ms/ms:0.02 tolerance, 0.0 offset (mono masses), 
theoretical_fragment_ions = 0
#
fragment_bin_tol = 1.0005  # binning to use on fragment ions
fragment_bin_offset = 0.4  # offset position to start the 
binning (0.0 to 1.0)
theoretical_fragment_ions = 1  # 0=use flanking peaks, 1=M peak only
use_A_ions = 0
use_B_ions = 1
use_C_ions = 0
use_X_ions = 0
use_Y_ions = 1
use_Z_ions = 0
use_NL_ions = 1# 0=no, 1=yes to consider NH3/H2O 
neutral loss peaks
use_sparse_matrix = 0

#
# output
#
output_sqtstream = 0   # 0=no, 1=yes  write sqt to standard 
output
output_sqtfile = 0 # 0=no, 1=yes  write sqt file
output_txtfile = 0 # 0=no, 1=yes  write tab-delimited 
txt file
output_pepxmlfile = 1  # 0=no, 1=yes  write pep.xml file
output_percolatorfile = 0  # 0=no, 1=yes  write Percolator 
tab-delimited input file
output_outfiles = 0# 0=no, 1=yes  write .out files
print_expect_score = 1 # 0=no, 1=yes to replace Sp with 
expect in out & sqt
num_output_lines = 5   # num peptide results to show
show_fragment_ions = 0 # 0=no, 1=yes for out files only

sample_enzyme_number = 1   # Sample enzyme which is possibly 
different than the one applied to the search.
   # Used to calculate NTT & NMC in 
pepXML output (default=1 for trypsin).

#
# mzXML parameters
#
scan_range = 0 0   # start and scan scan range to 
search; 0 as 1st entry ignores parameter
precursor_charge = 0 0 # precursor charge range to analyze; 
does not override any existing charge; 0 as 1st entry ignores parameter
override_charge = 0# 0=no, 1=yes to override existing 
precursor charge states with precursor_charge parameter
ms_level = 2   # MS level to analyze, valid are 
levels 2 (default) or 3
activation_method = ALL# activation method; used if 
activation method set; allowed ALL, CID, ECD, ETD, PQD, HCD, IRMPD

#
# misc parameters
#
digest_mass_range = 600.0 5000.0   # MH+ peptide mass range to analyze
num_results = 50   # number of search hits to store 
internally
skip_researching = 1   # for '.out' file output only, 
0=search everything again (default), 1=don't search if .out exists
max_fragment_charge = 3# set maximum fragment charge state 
to analyze (allowed max 5)
max_precursor_charge = 6   # set maximum precursor charge state 
to analyze (allowed max 9)
nucleotide_reading_frame = 0   # 0=proteinDB, 1-6, 7=forward three, 
8=reverse three, 9=all six
clip_nterm_methionine = 0  # 0=leave sequences as-is; 1=also 
consider sequence w/o N-term methionine
spectrum_batch_size = 0# max. # of spectra to search at a 
time; 0 to search the entire scan range in one loop
decoy_prefix = DECOY_  # decoy entries are denoted by this 
string which is pre-pended to each protein acc

RE: [spctools-discuss] Comet search performance issue

2016-03-21 Thread Michael Hoopmann 
Hi Bob,

Brian mentioned something that brought stalled applications to mind. Sometimes 
a virus scanner can halt the application at its start without warning you, 
leaving it in limbo indefinitely. If you are using a virus scanner, you can try 
disabling it to see if it solves the problem. If so, then create a rule that 
allows comet to run.

Cheers,

Mike

 

From: spctools-discuss@googlegroups.com 
[mailto:spctools-discuss@googlegroups.com] On Behalf Of Brian Hampton
Sent: Monday, March 21, 2016 3:39 PM
To: spctools-discuss
Subject: Re: [spctools-discuss] Comet search performance issue

 

Hello Bob,

Go to Task Manager and look at Processes to see if comet is still actually 
running.  If so look at Performance and see if it is using the number of 
threads that you specified in the parameter file.  This might give a clue as to 
why it is taking so long, for example if you somehow told it to use only one 
thread.  Did you specify an enzyme or no enzyme search? The latter will take a 
long time.  Might help if you posted your comet parameters file.

Also, I have found that running TPP processes from the command line produces 
useful output to help debug problems.  You can "cheat" and run it via Petunia, 
then copy paste the command from there to a cmd window and watch the output.  
Sometimes you will receive errors or warnings that will give you a clue as to 
what is happening.  You might also try generating a new comet params file and 
then editing it to suit your conditions.

WRT   msconvert, I usually just do peak picking on those MS levels where you 
have profile data and leave rest to defaults.  I am not certain what msconvert 
does with profile data by default so I specify that parameter.  It would be 
nice if others would share their msconvert parameters.

 

Brian








Brian Hampton
Protein Analysis Lab
Center for Vascular and Inflammatory Diseases
University of Maryland School of Medicine
655 West Baltimore Street BRB 7-018
Baltimore  MD  21201
V: 410-706-8207

 

On Mon, Mar 21, 2016 at 5:11 PM,  wrote:

Hi everyone,

 

I started a Comet search in TPP three days ago and it is still going three days 
later. I must have messed up something without knowing because TPP did not 
generate any error message. Did anyone else have similar experience? Please see 
my system and TPP info below.

 

HP Z600 Workstation

Windows 7 Professional

Processor: Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 2.66 GHz

Installed memory (RAM): 24.0 GB

System type: 64-bit Operating System

 

TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686)

 

Comet search

 

mzXML input file: mydata.mzXML (110 MB)

  generated using command line msconvert

  C:/Inetpub/tpp-bin/msconvert mydata.raw --mzXML --filter 
"mslevel 2" --filter "threshold count 100 most-intense"

  

Comet Parameters file: comet.params (default, came with TPP installation)

Sequence database: human_uniprot_sprot.fasta

 

Any advice/pointer is greatly appreciated.

 

Thanks,

 

Bob Xiong

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Re: [spctools-discuss] Comet search performance issue

2016-03-21 Thread Brian Hampton 
Hello Bob,

Go to Task Manager and look at Processes to see if comet is still actually
running.  If so look at Performance and see if it is using the number of
threads that you specified in the parameter file.  This might give a clue
as to why it is taking so long, for example if you somehow told it to use
only one thread.  Did you specify an enzyme or no enzyme search? The latter
will take a long time.  Might help if you posted your comet parameters file.

Also, I have found that running TPP processes from the command line
produces useful output to help debug problems.  You can "cheat" and run it
via Petunia, then copy paste the command from there to a cmd window and
watch the output.  Sometimes you will receive errors or warnings that will
give you a clue as to what is happening.  You might also try generating a
new comet params file and then editing it to suit your conditions.

WRT   msconvert, I usually just do peak picking on those MS levels where
you have profile data and leave rest to defaults.  I am not certain what
msconvert does with profile data by default so I specify that parameter.
It would be nice if others would share their msconvert parameters.

Brian




Brian Hampton
Protein Analysis Lab
Center for Vascular and Inflammatory Diseases
University of Maryland School of Medicine
655 West Baltimore Street BRB 7-018
Baltimore  MD  21201
V: 410-706-8207


On Mon, Mar 21, 2016 at 5:11 PM,  wrote:

> Hi everyone,
>
> I started a Comet search in TPP three days ago and it is still going three
> days later. I must have messed up something without knowing because TPP did
> not generate any error message. Did anyone else have similar experience?
> Please see my system and TPP info below.
>
> HP Z600 Workstation
> Windows 7 Professional
> Processor: Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 2.66 GHz
> Installed memory (RAM): 24.0 GB
> System type: 64-bit Operating System
>
> TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686)
>
> Comet search
>
> mzXML input file: mydata.mzXML (110 MB)
>   generated using command line msconvert
>   C:/Inetpub/tpp-bin/msconvert mydata.raw --mzXML --filter
> "mslevel 2" --filter "threshold count 100 most-intense"
>
> Comet Parameters file: comet.params (default, came with TPP installation)
> Sequence database: human_uniprot_sprot.fasta
>
> Any advice/pointer is greatly appreciated.
>
> Thanks,
>
> Bob Xiong
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
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Re: [spctools-discuss] Comet search performance issue

2016-03-21 Thread Jimmy Eng 
It would be helpful if you post (or send me) the search parameters which is
the contents of the comet.params file.

On Mon, Mar 21, 2016 at 2:11 PM,  wrote:

> Hi everyone,
>
> I started a Comet search in TPP three days ago and it is still going three
> days later. I must have messed up something without knowing because TPP did
> not generate any error message. Did anyone else have similar experience?
> Please see my system and TPP info below.
>
> HP Z600 Workstation
> Windows 7 Professional
> Processor: Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 2.66 GHz
> Installed memory (RAM): 24.0 GB
> System type: 64-bit Operating System
>
> TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686)
>
> Comet search
>
> mzXML input file: mydata.mzXML (110 MB)
>   generated using command line msconvert
>   C:/Inetpub/tpp-bin/msconvert mydata.raw --mzXML --filter
> "mslevel 2" --filter "threshold count 100 most-intense"
>
> Comet Parameters file: comet.params (default, came with TPP installation)
> Sequence database: human_uniprot_sprot.fasta
>
> Any advice/pointer is greatly appreciated.
>
> Thanks,
>
> Bob Xiong
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
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