Re: [spctools-discuss] how to continue or kill my jobs?

2015-04-22 Thread c qin
Thank you for your suggestion!


在 2015年4月18日星期六 UTC+8下午11:37:17,Jimmy Eng写道:
>
> Consider updating to "comet.2015011.win64.exe" from 
> "comet_binaries_2015011.zip" as searches should run faster.  The parameters 
> file will be slightly changed though so keep that in  mind.  Good luck.
>
> On Sat, Apr 18, 2015 at 2:17 AM, c qin > 
> wrote:
>
>> In fact, there is no error message, it was just stop and no changed when 
>> I click the "refresh". 
>> Because I attempt to repeat a process used the TPPv4.7.1 with 
>> comet2014010, as you said, I downloaded "comet_binaries_2014010.zip"and 
>> replaced the original comet.exe (C:\Inetpub\tpp-bin\) with 
>> comet.2014010.win64.exe 
>> from the zip,and rename it to "comet.exe". 
>> Surprisedly, as I restarted TPP and performed comet, it run well and 
>> completely! I clicked the "refresh" and it showed "search end" and "command 
>> successful"!
>> Gratitude beyond words, you help me a lot!
>>
>>
>>
>> 在 2015年4月15日星期三 UTC+8下午10:24:45,Jimmy Eng写道:
>>>
>>> Unless you post an error or log message or more descriptive information, 
>>> no one here will have any idea why your job "seems to be dead again".  But 
>>> you can try the following to see if it addresses the issues.
>>>
>>> Try setting  "spectrum_batch_size = 3000" and run again and see if that 
>>> changes anything.
>>>
>>> Another option to try is to update your Comet binary to the latest 
>>> version 2015.01 rev. 1 as the latest TPP distributes version 2014.02 rev. 
>>> 2.  Grab the file "comet_binaries_2015011.zip" from 
>>> http://sourceforge.net/projects/comet-ms/files/.  I believe the binary 
>>> you need to replace is at c:\inetpub\tpp-bin\comet.exe.  With this 2015.01 
>>> version, use these settings:
>>>
>>>fragment_bin_tol = 0.01
>>>use_sparse_matrix = 1
>>>spectrum_batch_size = 25000
>>>
>>> Good luck.
>>>
>>> On Wed, Apr 15, 2015 at 2:01 AM, c qin  wrote:
>>>
 Thank you so much. 
 It is high resolution data. it is the first time I use TPP and Comet, 
 and I just do this under the guidance of the article, the parameter file 
 is 
 dowloaded from PRIDE database and the data set identifier is PXD001126.

 fragment_bin_tol = 0.1

 use_sparse_matrix = 0

 spectrum_batch_size = 5000


 I perform TPP on win7(64bit) with  16G memory...

 在 2015年4月15日星期三 UTC+8下午1:08:02,Jimmy Eng写道:
>
> Is this high-res MS/MS data?  If so, what are your settings for the 
> following Comet search parameters?
>
>fragment_bin_tol
>use_sparse_matrix
>spectrum_batch_size
>
> And how much memory (RAM) does your computer have?
>
> - Jimmy
>
>
> On Tue, Apr 14, 2015 at 7:47 PM, c qin  wrote:
>
>> Thanks for your attention
>> now I can kill and delete my jobs,but when I start an other new 
>> job,it seems to be dead again,and the output file size stop being 
>> increased.
>> I`m sure it is not finished because the output file does not reach 
>> expected size like my reference artical showed...
>> Do you encounter this problem?
>>
>>
>> 在 2015年4月13日星期一 UTC+8下午12:35:43,andyzcq写道:
>>>
>>> Hi, I came across this issue and solved it in the following way.
>>> Find the TPP username folder (normally should 
>>> be C:\inetpub\tpp-bin\users\guest), and delete the file the name of 
>>> which contains the date of task.
>>> Note: do not delete .jobs and .password files.
>>> Hope it helps.
>>>
>>> On Sun, Apr 12, 2015 at 3:57 PM, c qin  wrote:
>>>

 *Hello,*

 Can I ask a question about TPP(Trans Proteomic Pipeline)?

 I run a job on the web of TPP several days ago,and it is running in 
 Database Search tab of Analysis Pipeline (Comet).However, until now,it 
 is 
 still in the running……
 My data size is about 3GB,and I do not feel it is too big. When I 
 click the “kill job” button,a messages show on orange window and tell 
 that “Unable 
 to kill command 3340! ()” 
 I have no idea what should I do to finish(continue or kill) my 
 job...


 Thank you
 c qin

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>>>
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Re: [spctools-discuss] how to continue or kill my jobs?

2015-04-18 Thread Jimmy Eng
Consider updating to "comet.2015011.win64.exe" from
"comet_binaries_2015011.zip" as searches should run faster.  The parameters
file will be slightly changed though so keep that in  mind.  Good luck.

On Sat, Apr 18, 2015 at 2:17 AM, c qin  wrote:

> In fact, there is no error message, it was just stop and no changed when I
> click the "refresh".
> Because I attempt to repeat a process used the TPPv4.7.1 with
> comet2014010, as you said, I downloaded "comet_binaries_2014010.zip"and
> replaced the original comet.exe (C:\Inetpub\tpp-bin\) with 
> comet.2014010.win64.exe
> from the zip,and rename it to "comet.exe".
> Surprisedly, as I restarted TPP and performed comet, it run well and
> completely! I clicked the "refresh" and it showed "search end" and "command
> successful"!
> Gratitude beyond words, you help me a lot!
>
>
>
> 在 2015年4月15日星期三 UTC+8下午10:24:45,Jimmy Eng写道:
>>
>> Unless you post an error or log message or more descriptive information,
>> no one here will have any idea why your job "seems to be dead again".  But
>> you can try the following to see if it addresses the issues.
>>
>> Try setting  "spectrum_batch_size = 3000" and run again and see if that
>> changes anything.
>>
>> Another option to try is to update your Comet binary to the latest
>> version 2015.01 rev. 1 as the latest TPP distributes version 2014.02 rev.
>> 2.  Grab the file "comet_binaries_2015011.zip" from
>> http://sourceforge.net/projects/comet-ms/files/.  I believe the binary
>> you need to replace is at c:\inetpub\tpp-bin\comet.exe.  With this 2015.01
>> version, use these settings:
>>
>>fragment_bin_tol = 0.01
>>use_sparse_matrix = 1
>>spectrum_batch_size = 25000
>>
>> Good luck.
>>
>> On Wed, Apr 15, 2015 at 2:01 AM, c qin  wrote:
>>
>>> Thank you so much.
>>> It is high resolution data. it is the first time I use TPP and Comet,
>>> and I just do this under the guidance of the article, the parameter file is
>>> dowloaded from PRIDE database and the data set identifier is PXD001126.
>>>
>>> fragment_bin_tol = 0.1
>>>
>>> use_sparse_matrix = 0
>>>
>>> spectrum_batch_size = 5000
>>>
>>>
>>> I perform TPP on win7(64bit) with  16G memory...
>>>
>>> 在 2015年4月15日星期三 UTC+8下午1:08:02,Jimmy Eng写道:

 Is this high-res MS/MS data?  If so, what are your settings for the
 following Comet search parameters?

fragment_bin_tol
use_sparse_matrix
spectrum_batch_size

 And how much memory (RAM) does your computer have?

 - Jimmy


 On Tue, Apr 14, 2015 at 7:47 PM, c qin  wrote:

> Thanks for your attention
> now I can kill and delete my jobs,but when I start an other new job,it
> seems to be dead again,and the output file size stop being increased.
> I`m sure it is not finished because the output file does not reach
> expected size like my reference artical showed...
> Do you encounter this problem?
>
>
> 在 2015年4月13日星期一 UTC+8下午12:35:43,andyzcq写道:
>>
>> Hi, I came across this issue and solved it in the following way.
>> Find the TPP username folder (normally should
>> be C:\inetpub\tpp-bin\users\guest), and delete the file the name of
>> which contains the date of task.
>> Note: do not delete .jobs and .password files.
>> Hope it helps.
>>
>> On Sun, Apr 12, 2015 at 3:57 PM, c qin  wrote:
>>
>>>
>>> *Hello,*
>>>
>>> Can I ask a question about TPP(Trans Proteomic Pipeline)?
>>>
>>> I run a job on the web of TPP several days ago,and it is running in
>>> Database Search tab of Analysis Pipeline (Comet).However, until now,it 
>>> is
>>> still in the running……
>>> My data size is about 3GB,and I do not feel it is too big. When I
>>> click the “kill job” button,a messages show on orange window and tell 
>>> that “Unable
>>> to kill command 3340! ()”
>>> I have no idea what should I do to finish(continue or kill) my job...
>>>
>>>
>>> Thank you
>>> c qin
>>>
>>> --
>>> 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-discu...@googlegroups.com.
>>> To post to this group, send email to spctools...@googlegroups.com.
>>> Visit this group at http://groups.google.com/group/spctools-discuss.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
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> For more options, visit https://groups.google.com/d/optout.
>


Re: [spctools-discuss] how to continue or kill my jobs?

2015-04-18 Thread c qin
In fact, there is no error message, it was just stop and no changed when I 
click the "refresh". 
Because I attempt to repeat a process used the TPPv4.7.1 with comet2014010, 
as you said, I downloaded "comet_binaries_2014010.zip"and replaced the 
original comet.exe (C:\Inetpub\tpp-bin\) with comet.2014010.win64.exe from 
the zip,and rename it to "comet.exe". 
Surprisedly, as I restarted TPP and performed comet, it run well and 
completely! I clicked the "refresh" and it showed "search end" and "command 
successful"!
Gratitude beyond words, you help me a lot!



在 2015年4月15日星期三 UTC+8下午10:24:45,Jimmy Eng写道:
>
> Unless you post an error or log message or more descriptive information, 
> no one here will have any idea why your job "seems to be dead again".  But 
> you can try the following to see if it addresses the issues.
>
> Try setting  "spectrum_batch_size = 3000" and run again and see if that 
> changes anything.
>
> Another option to try is to update your Comet binary to the latest version 
> 2015.01 rev. 1 as the latest TPP distributes version 2014.02 rev. 2.  Grab 
> the file "comet_binaries_2015011.zip" from 
> http://sourceforge.net/projects/comet-ms/files/.  I believe the binary 
> you need to replace is at c:\inetpub\tpp-bin\comet.exe.  With this 2015.01 
> version, use these settings:
>
>fragment_bin_tol = 0.01
>use_sparse_matrix = 1
>spectrum_batch_size = 25000
>
> Good luck.
>
> On Wed, Apr 15, 2015 at 2:01 AM, c qin > 
> wrote:
>
>> Thank you so much. 
>> It is high resolution data. it is the first time I use TPP and Comet, and 
>> I just do this under the guidance of the article, the parameter file is 
>> dowloaded from PRIDE database and the data set identifier is PXD001126.
>>
>> fragment_bin_tol = 0.1
>>
>> use_sparse_matrix = 0
>>
>> spectrum_batch_size = 5000
>>
>>
>> I perform TPP on win7(64bit) with  16G memory...
>>
>> 在 2015年4月15日星期三 UTC+8下午1:08:02,Jimmy Eng写道:
>>>
>>> Is this high-res MS/MS data?  If so, what are your settings for the 
>>> following Comet search parameters?
>>>
>>>fragment_bin_tol
>>>use_sparse_matrix
>>>spectrum_batch_size
>>>
>>> And how much memory (RAM) does your computer have?
>>>
>>> - Jimmy
>>>
>>>
>>> On Tue, Apr 14, 2015 at 7:47 PM, c qin  wrote:
>>>
 Thanks for your attention
 now I can kill and delete my jobs,but when I start an other new job,it 
 seems to be dead again,and the output file size stop being increased.
 I`m sure it is not finished because the output file does not reach 
 expected size like my reference artical showed...
 Do you encounter this problem?


 在 2015年4月13日星期一 UTC+8下午12:35:43,andyzcq写道:
>
> Hi, I came across this issue and solved it in the following way.
> Find the TPP username folder (normally should 
> be C:\inetpub\tpp-bin\users\guest), and delete the file the name of 
> which contains the date of task.
> Note: do not delete .jobs and .password files.
> Hope it helps.
>
> On Sun, Apr 12, 2015 at 3:57 PM, c qin  wrote:
>
>>
>> *Hello,*
>>
>> Can I ask a question about TPP(Trans Proteomic Pipeline)?
>>
>> I run a job on the web of TPP several days ago,and it is running in 
>> Database Search tab of Analysis Pipeline (Comet).However, until now,it 
>> is 
>> still in the running……
>> My data size is about 3GB,and I do not feel it is too big. When I 
>> click the “kill job” button,a messages show on orange window and tell 
>> that “Unable 
>> to kill command 3340! ()” 
>> I have no idea what should I do to finish(continue or kill) my job...
>>
>>
>> Thank you
>> c qin
>>
>> -- 
>> 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-discu...@googlegroups.com.
>> To post to this group, send email to spctools...@googlegroups.com.
>> Visit this group at http://groups.google.com/group/spctools-discuss.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  -- 
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 an email to spctools-discu...@googlegroups.com.
 To post to this group, send email to spctools...@googlegroups.com.
 Visit this group at http://groups.google.com/group/spctools-discuss.
 For more options, visit https://groups.google.com/d/optout.

>>>
>>>  -- 
>> 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 
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>> .
>> Visit this group at http://g

Re: [spctools-discuss] how to continue or kill my jobs?

2015-04-15 Thread Jimmy Eng
Unless you post an error or log message or more descriptive information, no
one here will have any idea why your job "seems to be dead again".  But you
can try the following to see if it addresses the issues.

Try setting  "spectrum_batch_size = 3000" and run again and see if that
changes anything.

Another option to try is to update your Comet binary to the latest version
2015.01 rev. 1 as the latest TPP distributes version 2014.02 rev. 2.  Grab
the file "comet_binaries_2015011.zip" from
http://sourceforge.net/projects/comet-ms/files/.  I believe the binary you
need to replace is at c:\inetpub\tpp-bin\comet.exe.  With this 2015.01
version, use these settings:

   fragment_bin_tol = 0.01
   use_sparse_matrix = 1
   spectrum_batch_size = 25000

Good luck.

On Wed, Apr 15, 2015 at 2:01 AM, c qin  wrote:

> Thank you so much.
> It is high resolution data. it is the first time I use TPP and Comet, and
> I just do this under the guidance of the article, the parameter file is
> dowloaded from PRIDE database and the data set identifier is PXD001126.
>
> fragment_bin_tol = 0.1
>
> use_sparse_matrix = 0
>
> spectrum_batch_size = 5000
>
>
> I perform TPP on win7(64bit) with  16G memory...
>
> 在 2015年4月15日星期三 UTC+8下午1:08:02,Jimmy Eng写道:
>>
>> Is this high-res MS/MS data?  If so, what are your settings for the
>> following Comet search parameters?
>>
>>fragment_bin_tol
>>use_sparse_matrix
>>spectrum_batch_size
>>
>> And how much memory (RAM) does your computer have?
>>
>> - Jimmy
>>
>>
>> On Tue, Apr 14, 2015 at 7:47 PM, c qin  wrote:
>>
>>> Thanks for your attention
>>> now I can kill and delete my jobs,but when I start an other new job,it
>>> seems to be dead again,and the output file size stop being increased.
>>> I`m sure it is not finished because the output file does not reach
>>> expected size like my reference artical showed...
>>> Do you encounter this problem?
>>>
>>>
>>> 在 2015年4月13日星期一 UTC+8下午12:35:43,andyzcq写道:

 Hi, I came across this issue and solved it in the following way.
 Find the TPP username folder (normally should
 be C:\inetpub\tpp-bin\users\guest), and delete the file the name of
 which contains the date of task.
 Note: do not delete .jobs and .password files.
 Hope it helps.

 On Sun, Apr 12, 2015 at 3:57 PM, c qin  wrote:

>
> *Hello,*
>
> Can I ask a question about TPP(Trans Proteomic Pipeline)?
>
> I run a job on the web of TPP several days ago,and it is running in
> Database Search tab of Analysis Pipeline (Comet).However, until now,it is
> still in the running……
> My data size is about 3GB,and I do not feel it is too big. When I
> click the “kill job” button,a messages show on orange window and tell 
> that “Unable
> to kill command 3340! ()”
> I have no idea what should I do to finish(continue or kill) my job...
>
>
> Thank you
> c qin
>
> --
> 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-discu...@googlegroups.com.
> To post to this group, send email to spctools...@googlegroups.com.
> Visit this group at http://groups.google.com/group/spctools-discuss.
> For more options, visit https://groups.google.com/d/optout.
>

  --
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>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
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Re: [spctools-discuss] how to continue or kill my jobs?

2015-04-15 Thread c qin
Thank you so much. 
It is high resolution data. it is the first time I use TPP and Comet, and I 
just do this under the guidance of the article, the parameter file is 
dowloaded from PRIDE database and the data set identifier is PXD001126.

fragment_bin_tol = 0.1

use_sparse_matrix = 0

spectrum_batch_size = 5000


I perform TPP on win7(64bit) with  16G memory...

在 2015年4月15日星期三 UTC+8下午1:08:02,Jimmy Eng写道:
>
> Is this high-res MS/MS data?  If so, what are your settings for the 
> following Comet search parameters?
>
>fragment_bin_tol
>use_sparse_matrix
>spectrum_batch_size
>
> And how much memory (RAM) does your computer have?
>
> - Jimmy
>
>
> On Tue, Apr 14, 2015 at 7:47 PM, c qin > 
> wrote:
>
>> Thanks for your attention
>> now I can kill and delete my jobs,but when I start an other new job,it 
>> seems to be dead again,and the output file size stop being increased.
>> I`m sure it is not finished because the output file does not reach 
>> expected size like my reference artical showed...
>> Do you encounter this problem?
>>
>>
>> 在 2015年4月13日星期一 UTC+8下午12:35:43,andyzcq写道:
>>>
>>> Hi, I came across this issue and solved it in the following way.
>>> Find the TPP username folder (normally should 
>>> be C:\inetpub\tpp-bin\users\guest), and delete the file the name of 
>>> which contains the date of task.
>>> Note: do not delete .jobs and .password files.
>>> Hope it helps.
>>>
>>> On Sun, Apr 12, 2015 at 3:57 PM, c qin  wrote:
>>>

 *Hello,*

 Can I ask a question about TPP(Trans Proteomic Pipeline)?

 I run a job on the web of TPP several days ago,and it is running in 
 Database Search tab of Analysis Pipeline (Comet).However, until now,it is 
 still in the running……
 My data size is about 3GB,and I do not feel it is too big. When I click 
 the “kill job” button,a messages show on orange window and tell that 
 “Unable 
 to kill command 3340! ()” 
 I have no idea what should I do to finish(continue or kill) my job...


 Thank you
 c qin

 -- 
 You received this message because you are subscribed to the Google 
 Groups "spctools-discuss" group.
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 To post to this group, send email to spctools...@googlegroups.com.
 Visit this group at http://groups.google.com/group/spctools-discuss.
 For more options, visit https://groups.google.com/d/optout.

>>>
>>>  -- 
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>> "spctools-discuss" group.
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>> email to spctools-discu...@googlegroups.com .
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>> For more options, visit https://groups.google.com/d/optout.
>>
>
>

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Re: [spctools-discuss] how to continue or kill my jobs?

2015-04-14 Thread Jimmy Eng
Is this high-res MS/MS data?  If so, what are your settings for the
following Comet search parameters?

   fragment_bin_tol
   use_sparse_matrix
   spectrum_batch_size

And how much memory (RAM) does your computer have?

- Jimmy


On Tue, Apr 14, 2015 at 7:47 PM, c qin  wrote:

> Thanks for your attention
> now I can kill and delete my jobs,but when I start an other new job,it
> seems to be dead again,and the output file size stop being increased.
> I`m sure it is not finished because the output file does not reach
> expected size like my reference artical showed...
> Do you encounter this problem?
>
>
> 在 2015年4月13日星期一 UTC+8下午12:35:43,andyzcq写道:
>>
>> Hi, I came across this issue and solved it in the following way.
>> Find the TPP username folder (normally should be 
>> C:\inetpub\tpp-bin\users\guest),
>> and delete the file the name of which contains the date of task.
>> Note: do not delete .jobs and .password files.
>> Hope it helps.
>>
>> On Sun, Apr 12, 2015 at 3:57 PM, c qin  wrote:
>>
>>>
>>> *Hello,*
>>>
>>> Can I ask a question about TPP(Trans Proteomic Pipeline)?
>>>
>>> I run a job on the web of TPP several days ago,and it is running in
>>> Database Search tab of Analysis Pipeline (Comet).However, until now,it is
>>> still in the running……
>>> My data size is about 3GB,and I do not feel it is too big. When I click
>>> the “kill job” button,a messages show on orange window and tell that “Unable
>>> to kill command 3340! ()”
>>> I have no idea what should I do to finish(continue or kill) my job...
>>>
>>>
>>> Thank you
>>> c qin
>>>
>>> --
>>> 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-discu...@googlegroups.com.
>>> To post to this group, send email to spctools...@googlegroups.com.
>>> Visit this group at http://groups.google.com/group/spctools-discuss.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
> You received this message because you are subscribed to the Google Groups
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Re: [spctools-discuss] how to continue or kill my jobs?

2015-04-14 Thread c qin
Thanks for your attention
now I can kill and delete my jobs,but when I start an other new job,it 
seems to be dead again,and the output file size stop being increased.
I`m sure it is not finished because the output file does not reach expected 
size like my reference artical showed...
Do you encounter this problem?


在 2015年4月13日星期一 UTC+8下午12:35:43,andyzcq写道:
>
> Hi, I came across this issue and solved it in the following way.
> Find the TPP username folder (normally should 
> be C:\inetpub\tpp-bin\users\guest), and delete the file the name of which 
> contains the date of task.
> Note: do not delete .jobs and .password files.
> Hope it helps.
>
> On Sun, Apr 12, 2015 at 3:57 PM, c qin > 
> wrote:
>
>>
>> *Hello,*
>>
>> Can I ask a question about TPP(Trans Proteomic Pipeline)?
>>
>> I run a job on the web of TPP several days ago,and it is running in 
>> Database Search tab of Analysis Pipeline (Comet).However, until now,it is 
>> still in the running……
>> My data size is about 3GB,and I do not feel it is too big. When I click 
>> the “kill job” button,a messages show on orange window and tell that “Unable 
>> to kill command 3340! ()” 
>> I have no idea what should I do to finish(continue or kill) my job...
>>
>>
>> Thank you
>> c qin
>>
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>>
>
>

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Re: [spctools-discuss] how to continue or kill my jobs?

2015-04-13 Thread c qin
it is very useful for me, thanks a lot for your help! ^_^

>
>

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Re: [spctools-discuss] how to continue or kill my jobs?

2015-04-12 Thread 钟传奇
Hi, I came across this issue and solved it in the following way.
Find the TPP username folder (normally should
be C:\inetpub\tpp-bin\users\guest), and delete the file the name of which
contains the date of task.
Note: do not delete .jobs and .password files.
Hope it helps.

On Sun, Apr 12, 2015 at 3:57 PM, c qin  wrote:

>
> *Hello,*
>
> Can I ask a question about TPP(Trans Proteomic Pipeline)?
>
> I run a job on the web of TPP several days ago,and it is running in
> Database Search tab of Analysis Pipeline (Comet).However, until now,it is
> still in the running……
> My data size is about 3GB,and I do not feel it is too big. When I click
> the “kill job” button,a messages show on orange window and tell that “Unable
> to kill command 3340! ()”
> I have no idea what should I do to finish(continue or kill) my job...
>
>
> Thank you
> c qin
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
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>

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