Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-07-19 Thread Zeyu Wang 
 Hi David,

Thank you!  I see my name in the release note.  I'm glad I could help 
optimize TPP usage. 
Regarding the CPU usage issue, I believe it is related to my Windows setup 
and not to Kojak or its settings. Moreover, this issue is tolerable and 
does not significantly affect the time required for searches. 

Best,
Zeyu Wang

On Thursday, July 18, 2024 at 5:41:28 PM UTC-4 David Shteynberg wrote:

> Zeyu,
>
> I think I was reading your message from May, about the issue which you 
> helped us identify and resolve, sorry.  Meanwhile,  I tested both MSVC 
> default version of Kojak and compared to the one built for TPP using gcc 
> and they seem completely equivalent in runtime.  Let me know if you observe 
> something different.
>
> Thank you,
> -David
>
> On Jul 18, 2024, at 2:33 PM, David Shteynberg  
> wrote:
>
> Hello Zeyu,
>
> Would you mind installing the latest update and report back if you still 
> have an issue here?
>
> Thanks,
> -David
>
> On Thu, Jul 18, 2024 at 1:35 PM Zeyu Wang  wrote:
>
>> Hi David,
>>
>> Sorry for the late reply. Later, I just left the computer running on 
>> E-cores, which took longer. Now I further tested the new kojak.exe you sent 
>> me, but it still doesn't change the default CPU usage.  
>>
>> I believe this "feature" is due to how Windows handles task 
>> prioritization. I finally resolved it by adjusting the priority and 
>> affinity of Kojak.exe in the Windows Task Manager. 
>>
>> Thanks for your help and advice!
>>
>> Best,
>> Zeyu Wang
>>
>> On Wednesday, May 29, 2024 at 10:52:42 PM UTC-4 David Shteynberg wrote:
>>
>>> Hi Zeyu,
>>>
>>> Thanks for testing this!  I recompiled another executable that should 
>>> use more of the CPU during the search.  Can you please test it to see if 
>>> this suits your needs?  Naturally, if you set the number of threads too 
>>> high it might degrade the overall performance of your machine during the 
>>> Kojak search.  
>>>
>>>
>>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>>>
>>> It would interesting to compare the performance of before and after this 
>>> change.  I am testing this on i9-13900H.
>>>
>>> Cheers,
>>> -David
>>>
>>> On Tue, May 28, 2024 at 9:21 PM Zeyu Wang  wrote:
>>>
 Hi David, 

 I tested it with the new version. Now it works well, but CPU usage 
 problem still exists. I change threads from 24, 20 to 16 and 8, but the 
 TPP 
 searching still uses E-cores. Perhaps it doesn't support P-Cores with 
 Intel 
 Hyper-Threading. I am just wondering what CPU you are using for Kojak.exe 
 running. 

 Thanks again! Anyway, it can still run, though may take a bit longer 
 time. 

 Best,
 Zeyu 

 On Tuesday, May 28, 2024 at 11:17:55 PM UTC-4 David Shteynberg wrote:

> Hello Zeyu,
>
> Sorry I don't know the answer to your question but if it helps I 
> corrected the issue you identified in the previously distributed version 
> compiled with gcc for the TPP distribution installer.
> I placed the gcc compiled version of Kojak.exe here: 
> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>
> Perhaps this one exhibits a different behavior when running 
> multi-threaded.  In my tests the two version ran nearly at the same speed 
> on my computer.
>
> Cheers,
> -David
>
> On Tue, May 28, 2024 at 7:27 PM Zeyu Wang  wrote:
>
>> Hi all,
>>
>> I notice another small issue (maybe this is my win11 problem?): when 
>> running Kojak within TPP, I set the threads to 24 or 28. However, in the 
>> task manager, I notice the main search was always running on exact 
>> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice 
>> similar problem?   
>>
>> [image: Snipaste_2024-05-28_22-14-14.png]
>> [image: Snipaste_2024-05-28_22-15-57.png]
>>
>> Best,
>> Zeyu 
>>
>>
>>
>>
>>
>> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:
>>
>>> Hi David,
>>>
>>> Thanks! After replacing the current kojak.exe, It seems that now the 
>>> kojak searching can continue without error message.
>>>
>>> Best,
>>> Zeyu 
>>>
>>> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:
>>>
 Hello again,

 After a bit of digging I found that this is likely caused by a bug 
 in the current TPP compiled and distributed version of Kojak that will 
 have 
 to be corrected for the next release.  Meanwhile you should be able to 
 download and use the official Kojak build available here:  
 https://kojak-ms.systemsbiology.net/download.html


 This version will require additional .net dependecies!

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-07-18 Thread David Shteynberg 
Zeyu,

I think I was reading your message from May, about the issue which you helped 
us identify and resolve, sorry.  Meanwhile,  I tested both MSVC default version 
of Kojak and compared to the one built for TPP using gcc and they seem 
completely equivalent in runtime.  Let me know if you observe something 
different.

Thank you,
-David

> On Jul 18, 2024, at 2:33 PM, David Shteynberg 
>  wrote:
> 
> Hello Zeyu,
> 
> Would you mind installing the latest update and report back if you still have 
> an issue here?
> 
> Thanks,
> -David
> 
> On Thu, Jul 18, 2024 at 1:35 PM Zeyu Wang  > wrote:
>> Hi David,
>> 
>> Sorry for the late reply. Later, I just left the computer running on 
>> E-cores, which took longer. Now I further tested the new kojak.exe you sent 
>> me, but it still doesn't change the default CPU usage.  
>> 
>> I believe this "feature" is due to how Windows handles task prioritization. 
>> I finally resolved it by adjusting the priority and affinity of Kojak.exe in 
>> the Windows Task Manager. 
>> 
>> Thanks for your help and advice!
>> 
>> Best,
>> Zeyu Wang
>> 
>> On Wednesday, May 29, 2024 at 10:52:42 PM UTC-4 David Shteynberg wrote:
>>> Hi Zeyu,
>>> 
>>> Thanks for testing this!  I recompiled another executable that should use 
>>> more of the CPU during the search.  Can you please test it to see if this 
>>> suits your needs?  Naturally, if you set the number of threads too high it 
>>> might degrade the overall performance of your machine during the Kojak 
>>> search.  
>>> 
>>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>>> 
>>> It would interesting to compare the performance of before and after this 
>>> change.  I am testing this on i9-13900H.
>>> 
>>> Cheers,
>>> -David
>>> 
>>> On Tue, May 28, 2024 at 9:21 PM Zeyu Wang > wrote:
 Hi David, 
 
 I tested it with the new version. Now it works well, but CPU usage problem 
 still exists. I change threads from 24, 20 to 16 and 8, but the TPP 
 searching still uses E-cores. Perhaps it doesn't support P-Cores with 
 Intel Hyper-Threading. I am just wondering what CPU you are using for 
 Kojak.exe running. 
 
 Thanks again! Anyway, it can still run, though may take a bit longer time. 
 
 Best,
 Zeyu 
 
 On Tuesday, May 28, 2024 at 11:17:55 PM UTC-4 David Shteynberg wrote:
> Hello Zeyu,
> 
> Sorry I don't know the answer to your question but if it helps I 
> corrected the issue you identified in the previously distributed version 
> compiled with gcc for the TPP distribution installer.
> I placed the gcc compiled version of Kojak.exe here: 
> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
> 
> Perhaps this one exhibits a different behavior when running 
> multi-threaded.  In my tests the two version ran nearly at the same speed 
> on my computer.
> 
> Cheers,
> -David
> 
> On Tue, May 28, 2024 at 7:27 PM Zeyu Wang > wrote:
>> Hi all,
>> 
>> I notice another small issue (maybe this is my win11 problem?): when 
>> running Kojak within TPP, I set the threads to 24 or 28. However, in the 
>> task manager, I notice the main search was always running on exact 
>> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice 
>> similar problem?   
>> 
>> 
>> 
>> 
>> Best,
>> Zeyu 
>> 
>> 
>> 
>> 
>> 
>> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:
>>> Hi David,
>>> 
>>> Thanks! After replacing the current kojak.exe, It seems that now the 
>>> kojak searching can continue without error message.
>>> 
>>> Best,
>>> Zeyu 
>>> 
>>> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:
 Hello again,
 
 After a bit of digging I found that this is likely caused by a bug in 
 the current TPP compiled and distributed version of Kojak that will 
 have to be corrected for the next release.  Meanwhile you should be 
 able to download and use the official Kojak build available here:  
 https://kojak-ms.systemsbiology.net/download.html
 
 
 This version will require additional .net dependecies!
 
 Please replace the current kojak executable in c:/TPP/bin with the 
 executable from the zip file and try running kojak again.
 
 
 Best of luck and keep us posted to your progress.
 
 -David
 
 On Fri, May 24, 2024, 1:07 PM Zeyu Wang > wrote:
> Hi David,
> 
> Thank you! Here are the two kojak parameter files I tested (the 
> original and the customized).  Link: Kojak_Troubleshooting 
>

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-07-18 Thread 'David Shteynberg' via spctools-discuss 
Hello Zeyu,

Would you mind installing the latest update and report back if you still
have an issue here?

Thanks,
-David

On Thu, Jul 18, 2024 at 1:35 PM Zeyu Wang  wrote:

> Hi David,
>
> Sorry for the late reply. Later, I just left the computer running on
> E-cores, which took longer. Now I further tested the new kojak.exe you sent
> me, but it still doesn't change the default CPU usage.
>
> I believe this "feature" is due to how Windows handles task
> prioritization. I finally resolved it by adjusting the priority and
> affinity of Kojak.exe in the Windows Task Manager.
>
> Thanks for your help and advice!
>
> Best,
> Zeyu Wang
>
> On Wednesday, May 29, 2024 at 10:52:42 PM UTC-4 David Shteynberg wrote:
>
>> Hi Zeyu,
>>
>> Thanks for testing this!  I recompiled another executable that should use
>> more of the CPU during the search.  Can you please test it to see if this
>> suits your needs?  Naturally, if you set the number of threads too high it
>> might degrade the overall performance of your machine during the Kojak
>> search.
>>
>>
>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>>
>> It would interesting to compare the performance of before and after this
>> change.  I am testing this on i9-13900H.
>>
>> Cheers,
>> -David
>>
>> On Tue, May 28, 2024 at 9:21 PM Zeyu Wang  wrote:
>>
>>> Hi David,
>>>
>>> I tested it with the new version. Now it works well, but CPU usage
>>> problem still exists. I change threads from 24, 20 to 16 and 8, but the TPP
>>> searching still uses E-cores. Perhaps it doesn't support P-Cores with Intel
>>> Hyper-Threading. I am just wondering what CPU you are using for Kojak.exe
>>> running.
>>>
>>> Thanks again! Anyway, it can still run, though may take a bit longer
>>> time.
>>>
>>> Best,
>>> Zeyu
>>>
>>> On Tuesday, May 28, 2024 at 11:17:55 PM UTC-4 David Shteynberg wrote:
>>>
 Hello Zeyu,

 Sorry I don't know the answer to your question but if it helps I
 corrected the issue you identified in the previously distributed version
 compiled with gcc for the TPP distribution installer.
 I placed the gcc compiled version of Kojak.exe here:
 https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download

 Perhaps this one exhibits a different behavior when running
 multi-threaded.  In my tests the two version ran nearly at the same speed
 on my computer.

 Cheers,
 -David

 On Tue, May 28, 2024 at 7:27 PM Zeyu Wang  wrote:

> Hi all,
>
> I notice another small issue (maybe this is my win11 problem?): when
> running Kojak within TPP, I set the threads to 24 or 28. However, in the
> task manager, I notice the main search was always running on exact
> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice
> similar problem?
>
> [image: Snipaste_2024-05-28_22-14-14.png]
> [image: Snipaste_2024-05-28_22-15-57.png]
>
> Best,
> Zeyu
>
>
>
>
>
> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:
>
>> Hi David,
>>
>> Thanks! After replacing the current kojak.exe, It seems that now the
>> kojak searching can continue without error message.
>>
>> Best,
>> Zeyu
>>
>> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:
>>
>>> Hello again,
>>>
>>> After a bit of digging I found that this is likely caused by a bug
>>> in the current TPP compiled and distributed version of Kojak that will 
>>> have
>>> to be corrected for the next release.  Meanwhile you should be able to
>>> download and use the official Kojak build available here:
>>> https://kojak-ms.systemsbiology.net/download.html
>>>
>>>
>>> This version will require additional .net dependecies!
>>>
>>> Please replace the current kojak executable in c:/TPP/bin with the
>>> executable from the zip file and try running kojak again.
>>>
>>>
>>> Best of luck and keep us posted to your progress.
>>>
>>> -David
>>>
>>> On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:
>>>
 Hi David,

 Thank you! Here are the two kojak parameter files I tested (the
 original and the customized).  Link: Kojak_Troubleshooting
 
  .

 Best,
 Zeyu







 On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:

 Hello Zeyu,

 Thanks for your interest in TPP and Kojak.  Yes we maintain and use
 Kojak in the latest release.  To help us troubleshoot this problem, 
 would
>

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-07-18 Thread Zeyu Wang 
Hi David,

Sorry for the late reply. Later, I just left the computer running on 
E-cores, which took longer. Now I further tested the new kojak.exe you sent 
me, but it still doesn't change the default CPU usage.  

I believe this "feature" is due to how Windows handles task prioritization. 
I finally resolved it by adjusting the priority and affinity of Kojak.exe 
in the Windows Task Manager. 

Thanks for your help and advice!

Best,
Zeyu Wang

On Wednesday, May 29, 2024 at 10:52:42 PM UTC-4 David Shteynberg wrote:

> Hi Zeyu,
>
> Thanks for testing this!  I recompiled another executable that should use 
> more of the CPU during the search.  Can you please test it to see if this 
> suits your needs?  Naturally, if you set the number of threads too high it 
> might degrade the overall performance of your machine during the Kojak 
> search.  
>
>
> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>
> It would interesting to compare the performance of before and after this 
> change.  I am testing this on i9-13900H.
>
> Cheers,
> -David
>
> On Tue, May 28, 2024 at 9:21 PM Zeyu Wang  wrote:
>
>> Hi David, 
>>
>> I tested it with the new version. Now it works well, but CPU usage 
>> problem still exists. I change threads from 24, 20 to 16 and 8, but the TPP 
>> searching still uses E-cores. Perhaps it doesn't support P-Cores with Intel 
>> Hyper-Threading. I am just wondering what CPU you are using for Kojak.exe 
>> running. 
>>
>> Thanks again! Anyway, it can still run, though may take a bit longer 
>> time. 
>>
>> Best,
>> Zeyu 
>>
>> On Tuesday, May 28, 2024 at 11:17:55 PM UTC-4 David Shteynberg wrote:
>>
>>> Hello Zeyu,
>>>
>>> Sorry I don't know the answer to your question but if it helps I 
>>> corrected the issue you identified in the previously distributed version 
>>> compiled with gcc for the TPP distribution installer.
>>> I placed the gcc compiled version of Kojak.exe here: 
>>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>>>
>>> Perhaps this one exhibits a different behavior when running 
>>> multi-threaded.  In my tests the two version ran nearly at the same speed 
>>> on my computer.
>>>
>>> Cheers,
>>> -David
>>>
>>> On Tue, May 28, 2024 at 7:27 PM Zeyu Wang  wrote:
>>>
 Hi all,

 I notice another small issue (maybe this is my win11 problem?): when 
 running Kojak within TPP, I set the threads to 24 or 28. However, in the 
 task manager, I notice the main search was always running on exact 
 CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice 
 similar problem?   

 [image: Snipaste_2024-05-28_22-14-14.png]
 [image: Snipaste_2024-05-28_22-15-57.png]

 Best,
 Zeyu 





 On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:

> Hi David,
>
> Thanks! After replacing the current kojak.exe, It seems that now the 
> kojak searching can continue without error message.
>
> Best,
> Zeyu 
>
> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:
>
>> Hello again,
>>
>> After a bit of digging I found that this is likely caused by a bug in 
>> the current TPP compiled and distributed version of Kojak that will have 
>> to 
>> be corrected for the next release.  Meanwhile you should be able to 
>> download and use the official Kojak build available here:  
>> https://kojak-ms.systemsbiology.net/download.html
>>
>>
>> This version will require additional .net dependecies!
>>
>> Please replace the current kojak executable in c:/TPP/bin with the 
>> executable from the zip file and try running kojak again.
>>
>>
>> Best of luck and keep us posted to your progress.
>>
>> -David
>>
>> On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:
>>
>>> Hi David,
>>>
>>> Thank you! Here are the two kojak parameter files I tested (the 
>>> original and the customized).  Link: Kojak_Troubleshooting 
>>> 
>>>  .
>>>
>>> Best,
>>> Zeyu 
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:
>>>
>>> Hello Zeyu,
>>>
>>> Thanks for your interest in TPP and Kojak.  Yes we maintain and use 
>>> Kojak in the latest release.  To help us troubleshoot this problem, 
>>> would 
>>> you mind sharing the parameter file used in your test?
>>>
>>> Thank you!
>>> -David
>>>
>>> On Fri, May 24, 2024, 12:28 AM Zeyu Wang  
>>> wrote:
>>>
>>> Hi,
>>>
>>> Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow t

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-05-29 Thread 'David Shteynberg' via spctools-discuss 
Hi Zeyu,

Thanks for testing this!  I recompiled another executable that should use
more of the CPU during the search.  Can you please test it to see if this
suits your needs?  Naturally, if you set the number of threads too high it
might degrade the overall performance of your machine during the Kojak
search.

https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download

It would interesting to compare the performance of before and after this
change.  I am testing this on i9-13900H.

Cheers,
-David

On Tue, May 28, 2024 at 9:21 PM Zeyu Wang  wrote:

> Hi David,
>
> I tested it with the new version. Now it works well, but CPU usage problem
> still exists. I change threads from 24, 20 to 16 and 8, but the TPP
> searching still uses E-cores. Perhaps it doesn't support P-Cores with Intel
> Hyper-Threading. I am just wondering what CPU you are using for Kojak.exe
> running.
>
> Thanks again! Anyway, it can still run, though may take a bit longer time.
>
> Best,
> Zeyu
>
> On Tuesday, May 28, 2024 at 11:17:55 PM UTC-4 David Shteynberg wrote:
>
>> Hello Zeyu,
>>
>> Sorry I don't know the answer to your question but if it helps I
>> corrected the issue you identified in the previously distributed version
>> compiled with gcc for the TPP distribution installer.
>> I placed the gcc compiled version of Kojak.exe here:
>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>>
>> Perhaps this one exhibits a different behavior when running
>> multi-threaded.  In my tests the two version ran nearly at the same speed
>> on my computer.
>>
>> Cheers,
>> -David
>>
>> On Tue, May 28, 2024 at 7:27 PM Zeyu Wang  wrote:
>>
>>> Hi all,
>>>
>>> I notice another small issue (maybe this is my win11 problem?): when
>>> running Kojak within TPP, I set the threads to 24 or 28. However, in the
>>> task manager, I notice the main search was always running on exact
>>> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice
>>> similar problem?
>>>
>>> [image: Snipaste_2024-05-28_22-14-14.png]
>>> [image: Snipaste_2024-05-28_22-15-57.png]
>>>
>>> Best,
>>> Zeyu
>>>
>>>
>>>
>>>
>>>
>>> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:
>>>
 Hi David,

 Thanks! After replacing the current kojak.exe, It seems that now the
 kojak searching can continue without error message.

 Best,
 Zeyu

 On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:

> Hello again,
>
> After a bit of digging I found that this is likely caused by a bug in
> the current TPP compiled and distributed version of Kojak that will have 
> to
> be corrected for the next release.  Meanwhile you should be able to
> download and use the official Kojak build available here:
> https://kojak-ms.systemsbiology.net/download.html
>
>
> This version will require additional .net dependecies!
>
> Please replace the current kojak executable in c:/TPP/bin with the
> executable from the zip file and try running kojak again.
>
>
> Best of luck and keep us posted to your progress.
>
> -David
>
> On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:
>
>> Hi David,
>>
>> Thank you! Here are the two kojak parameter files I tested (the
>> original and the customized).  Link: Kojak_Troubleshooting
>> 
>>  .
>>
>> Best,
>> Zeyu
>>
>>
>>
>>
>>
>>
>>
>> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:
>>
>> Hello Zeyu,
>>
>> Thanks for your interest in TPP and Kojak.  Yes we maintain and use
>> Kojak in the latest release.  To help us troubleshoot this problem, would
>> you mind sharing the parameter file used in your test?
>>
>> Thank you!
>> -David
>>
>> On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:
>>
>> Hi,
>>
>> Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the
>> instruction and try to run a quick test. But at the very beginning, it
>> reports an error.
>>
>> "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann,
>> Institute for Systems Biology Visit http://kojak-ms.org for full
>> documentation. ** Begin Kojak Analysis ** Time at start: Fri May 
>> 24
>> 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12
>> preconfigured crosslinkers. Reading FASTA database:
>> c:/TPP/data/dbase/UP05640_9606_20230222.fasta
>> ...
>>   Total Proteins: 20594
>>   Adding Kojak-generated decoys. New Total Proteins: 41188
>>   5658462 peptides to search (2785870 linkable).
>>
>> Fri May 24 02:52:45

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-05-28 Thread Zeyu Wang 
Hi David, 

I tested it with the new version. Now it works well, but CPU usage problem 
still exists. I change threads from 24, 20 to 16 and 8, but the TPP 
searching still uses E-cores. Perhaps it doesn't support P-Cores with Intel 
Hyper-Threading. I am just wondering what CPU you are using for Kojak.exe 
running. 

Thanks again! Anyway, it can still run, though may take a bit longer time. 

Best,
Zeyu 

On Tuesday, May 28, 2024 at 11:17:55 PM UTC-4 David Shteynberg wrote:

> Hello Zeyu,
>
> Sorry I don't know the answer to your question but if it helps I corrected 
> the issue you identified in the previously distributed version compiled 
> with gcc for the TPP distribution installer.
> I placed the gcc compiled version of Kojak.exe here: 
> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>
> Perhaps this one exhibits a different behavior when running 
> multi-threaded.  In my tests the two version ran nearly at the same speed 
> on my computer.
>
> Cheers,
> -David
>
> On Tue, May 28, 2024 at 7:27 PM Zeyu Wang  wrote:
>
>> Hi all,
>>
>> I notice another small issue (maybe this is my win11 problem?): when 
>> running Kojak within TPP, I set the threads to 24 or 28. However, in the 
>> task manager, I notice the main search was always running on exact 
>> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice 
>> similar problem?   
>>
>> [image: Snipaste_2024-05-28_22-14-14.png]
>> [image: Snipaste_2024-05-28_22-15-57.png]
>>
>> Best,
>> Zeyu 
>>
>>
>>
>>
>>
>> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:
>>
>>> Hi David,
>>>
>>> Thanks! After replacing the current kojak.exe, It seems that now the 
>>> kojak searching can continue without error message.
>>>
>>> Best,
>>> Zeyu 
>>>
>>> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:
>>>
 Hello again,

 After a bit of digging I found that this is likely caused by a bug in 
 the current TPP compiled and distributed version of Kojak that will have 
 to 
 be corrected for the next release.  Meanwhile you should be able to 
 download and use the official Kojak build available here:  
 https://kojak-ms.systemsbiology.net/download.html


 This version will require additional .net dependecies!

 Please replace the current kojak executable in c:/TPP/bin with the 
 executable from the zip file and try running kojak again.


 Best of luck and keep us posted to your progress.

 -David

 On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:

> Hi David,
>
> Thank you! Here are the two kojak parameter files I tested (the 
> original and the customized).  Link: Kojak_Troubleshooting 
> 
>  .
>
> Best,
> Zeyu 
>
>
>
>
>
>
>
> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:
>
> Hello Zeyu,
>
> Thanks for your interest in TPP and Kojak.  Yes we maintain and use 
> Kojak in the latest release.  To help us troubleshoot this problem, would 
> you mind sharing the parameter file used in your test?
>
> Thank you!
> -David
>
> On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:
>
> Hi,
>
> Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the 
> instruction and try to run a quick test. But at the very beginning, it 
> reports an error. 
>
> "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann, 
> Institute for Systems Biology Visit http://kojak-ms.org for full 
> documentation. ** Begin Kojak Analysis ** Time at start: Fri May 
> 24 
> 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12 
> preconfigured crosslinkers. Reading FASTA database: 
> c:/TPP/data/dbase/UP05640_9606_20230222.fasta
> ...
>   Total Proteins: 20594
>   Adding Kojak-generated decoys. New Total Proteins: 41188
>   5658462 peptides to search (2785870 linkable).
>
> Fri May 24 02:52:45 2024 ERROR: 
> ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt 
> for output. Please ensure path and write permissions are correct."
>
> Is the error due to the output file path format? Or shall I adjust the 
> read/write permission of the TPP?
>
> Best,
> Zeyu
>
> -- 
> 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 view this discussion on the web visit 
> https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.co

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-05-28 Thread Zeyu Wang 
Hi David,

Thank you! I will replace the previous Kojak.exe (official build) with this 
new gcc compiled version and have a try.  

Best,
Zeyu  

On Tuesday, May 28, 2024 at 11:17:55 PM UTC-4 David Shteynberg wrote:

> Hello Zeyu,
>
> Sorry I don't know the answer to your question but if it helps I corrected 
> the issue you identified in the previously distributed version compiled 
> with gcc for the TPP distribution installer.
> I placed the gcc compiled version of Kojak.exe here: 
> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>
> Perhaps this one exhibits a different behavior when running 
> multi-threaded.  In my tests the two version ran nearly at the same speed 
> on my computer.
>
> Cheers,
> -David
>
> On Tue, May 28, 2024 at 7:27 PM Zeyu Wang  wrote:
>
>> Hi all,
>>
>> I notice another small issue (maybe this is my win11 problem?): when 
>> running Kojak within TPP, I set the threads to 24 or 28. However, in the 
>> task manager, I notice the main search was always running on exact 
>> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice 
>> similar problem?   
>>
>> [image: Snipaste_2024-05-28_22-14-14.png]
>> [image: Snipaste_2024-05-28_22-15-57.png]
>>
>> Best,
>> Zeyu 
>>
>>
>>
>>
>>
>> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:
>>
>>> Hi David,
>>>
>>> Thanks! After replacing the current kojak.exe, It seems that now the 
>>> kojak searching can continue without error message.
>>>
>>> Best,
>>> Zeyu 
>>>
>>> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:
>>>
 Hello again,

 After a bit of digging I found that this is likely caused by a bug in 
 the current TPP compiled and distributed version of Kojak that will have 
 to 
 be corrected for the next release.  Meanwhile you should be able to 
 download and use the official Kojak build available here:  
 https://kojak-ms.systemsbiology.net/download.html


 This version will require additional .net dependecies!

 Please replace the current kojak executable in c:/TPP/bin with the 
 executable from the zip file and try running kojak again.


 Best of luck and keep us posted to your progress.

 -David

 On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:

> Hi David,
>
> Thank you! Here are the two kojak parameter files I tested (the 
> original and the customized).  Link: Kojak_Troubleshooting 
> 
>  .
>
> Best,
> Zeyu 
>
>
>
>
>
>
>
> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:
>
> Hello Zeyu,
>
> Thanks for your interest in TPP and Kojak.  Yes we maintain and use 
> Kojak in the latest release.  To help us troubleshoot this problem, would 
> you mind sharing the parameter file used in your test?
>
> Thank you!
> -David
>
> On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:
>
> Hi,
>
> Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the 
> instruction and try to run a quick test. But at the very beginning, it 
> reports an error. 
>
> "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann, 
> Institute for Systems Biology Visit http://kojak-ms.org for full 
> documentation. ** Begin Kojak Analysis ** Time at start: Fri May 
> 24 
> 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12 
> preconfigured crosslinkers. Reading FASTA database: 
> c:/TPP/data/dbase/UP05640_9606_20230222.fasta
> ...
>   Total Proteins: 20594
>   Adding Kojak-generated decoys. New Total Proteins: 41188
>   5658462 peptides to search (2785870 linkable).
>
> Fri May 24 02:52:45 2024 ERROR: 
> ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt 
> for output. Please ensure path and write permissions are correct."
>
> Is the error due to the output file path format? Or shall I adjust the 
> read/write permission of the TPP?
>
> Best,
> Zeyu
>
> -- 
> 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 view this discussion on the web visit 
> https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.com
>  
> 
> .
>
> -- 
> You received this message because you are subscribed to the Google 
>

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-05-28 Thread 'David Shteynberg' via spctools-discuss 
Hello Zeyu,

Sorry I don't know the answer to your question but if it helps I corrected
the issue you identified in the previously distributed version compiled
with gcc for the TPP distribution installer.
I placed the gcc compiled version of Kojak.exe here:
https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download

Perhaps this one exhibits a different behavior when running
multi-threaded.  In my tests the two version ran nearly at the same speed
on my computer.

Cheers,
-David

On Tue, May 28, 2024 at 7:27 PM Zeyu Wang  wrote:

> Hi all,
>
> I notice another small issue (maybe this is my win11 problem?): when
> running Kojak within TPP, I set the threads to 24 or 28. However, in the
> task manager, I notice the main search was always running on exact
> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice
> similar problem?
>
> [image: Snipaste_2024-05-28_22-14-14.png]
> [image: Snipaste_2024-05-28_22-15-57.png]
>
> Best,
> Zeyu
>
>
>
>
>
> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:
>
>> Hi David,
>>
>> Thanks! After replacing the current kojak.exe, It seems that now the
>> kojak searching can continue without error message.
>>
>> Best,
>> Zeyu
>>
>> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:
>>
>>> Hello again,
>>>
>>> After a bit of digging I found that this is likely caused by a bug in
>>> the current TPP compiled and distributed version of Kojak that will have to
>>> be corrected for the next release.  Meanwhile you should be able to
>>> download and use the official Kojak build available here:
>>> https://kojak-ms.systemsbiology.net/download.html
>>>
>>>
>>> This version will require additional .net dependecies!
>>>
>>> Please replace the current kojak executable in c:/TPP/bin with the
>>> executable from the zip file and try running kojak again.
>>>
>>>
>>> Best of luck and keep us posted to your progress.
>>>
>>> -David
>>>
>>> On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:
>>>
 Hi David,

 Thank you! Here are the two kojak parameter files I tested (the
 original and the customized).  Link: Kojak_Troubleshooting
 
  .

 Best,
 Zeyu







 On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:

 Hello Zeyu,

 Thanks for your interest in TPP and Kojak.  Yes we maintain and use
 Kojak in the latest release.  To help us troubleshoot this problem, would
 you mind sharing the parameter file used in your test?

 Thank you!
 -David

 On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:

 Hi,

 Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the
 instruction and try to run a quick test. But at the very beginning, it
 reports an error.

 "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann,
 Institute for Systems Biology Visit http://kojak-ms.org for full
 documentation. ** Begin Kojak Analysis ** Time at start: Fri May 24
 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12
 preconfigured crosslinkers. Reading FASTA database:
 c:/TPP/data/dbase/UP05640_9606_20230222.fasta
 ...
   Total Proteins: 20594
   Adding Kojak-generated decoys. New Total Proteins: 41188
   5658462 peptides to search (2785870 linkable).

 Fri May 24 02:52:45 2024 ERROR:
 ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt
 for output. Please ensure path and write permissions are correct."

 Is the error due to the output file path format? Or shall I adjust the
 read/write permission of the TPP?

 Best,
 Zeyu

 --
 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 view this discussion on the web visit
 https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.com
 
 .

 --
 You received this message because you are subscribed to the Google
 Groups "spctools-discuss" group.
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 an email to spctools-discu...@googlegroups.com.

>>> To view this discussion on the web visit
 https://groups.google.com/d/msgid/spctools-discuss/9f93e2d2-c59b-4ed9-8813-4728ca2e4a16n%40googlegroups.com

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-05-28 Thread Zeyu Wang 
Hi all,

I notice another small issue (maybe this is my win11 problem?): when 
running Kojak within TPP, I set the threads to 24 or 28. However, in the 
task manager, I notice the main search was always running on exact 
CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice 
similar problem?   

[image: Snipaste_2024-05-28_22-14-14.png]
[image: Snipaste_2024-05-28_22-15-57.png]

Best,
Zeyu 





On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:

> Hi David,
>
> Thanks! After replacing the current kojak.exe, It seems that now the kojak 
> searching can continue without error message.
>
> Best,
> Zeyu 
>
> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:
>
>> Hello again,
>>
>> After a bit of digging I found that this is likely caused by a bug in the 
>> current TPP compiled and distributed version of Kojak that will have to be 
>> corrected for the next release.  Meanwhile you should be able to download 
>> and use the official Kojak build available here:  
>> https://kojak-ms.systemsbiology.net/download.html
>>
>>
>> This version will require additional .net dependecies!
>>
>> Please replace the current kojak executable in c:/TPP/bin with the 
>> executable from the zip file and try running kojak again.
>>
>>
>> Best of luck and keep us posted to your progress.
>>
>> -David
>>
>> On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:
>>
>>> Hi David,
>>>
>>> Thank you! Here are the two kojak parameter files I tested (the original 
>>> and the customized).  Link: Kojak_Troubleshooting 
>>> 
>>>  .
>>>
>>> Best,
>>> Zeyu 
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:
>>>
>>> Hello Zeyu,
>>>
>>> Thanks for your interest in TPP and Kojak.  Yes we maintain and use 
>>> Kojak in the latest release.  To help us troubleshoot this problem, would 
>>> you mind sharing the parameter file used in your test?
>>>
>>> Thank you!
>>> -David
>>>
>>> On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:
>>>
>>> Hi,
>>>
>>> Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the 
>>> instruction and try to run a quick test. But at the very beginning, it 
>>> reports an error. 
>>>
>>> "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann, 
>>> Institute for Systems Biology Visit http://kojak-ms.org for full 
>>> documentation. ** Begin Kojak Analysis ** Time at start: Fri May 24 
>>> 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12 
>>> preconfigured crosslinkers. Reading FASTA database: 
>>> c:/TPP/data/dbase/UP05640_9606_20230222.fasta
>>> ...
>>>   Total Proteins: 20594
>>>   Adding Kojak-generated decoys. New Total Proteins: 41188
>>>   5658462 peptides to search (2785870 linkable).
>>>
>>> Fri May 24 02:52:45 2024 ERROR: 
>>> ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt for 
>>> output. Please ensure path and write permissions are correct."
>>>
>>> Is the error due to the output file path format? Or shall I adjust the 
>>> read/write permission of the TPP?
>>>
>>> Best,
>>> Zeyu
>>>
>>> -- 
>>> 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 view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.com
>>>  
>>> 
>>> .
>>>
>>> -- 
>>> 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 view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/spctools-discuss/9f93e2d2-c59b-4ed9-8813-4728ca2e4a16n%40googlegroups.com
>>>  
>>> 
>>> .
>>>
>>

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Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-05-27 Thread Zeyu Wang 
Hi David,

Thanks! After replacing the current kojak.exe, It seems that now the kojak 
searching can continue without error message.

Best,
Zeyu 

On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:

> Hello again,
>
> After a bit of digging I found that this is likely caused by a bug in the 
> current TPP compiled and distributed version of Kojak that will have to be 
> corrected for the next release.  Meanwhile you should be able to download 
> and use the official Kojak build available here:  
> https://kojak-ms.systemsbiology.net/download.html
>
>
> This version will require additional .net dependecies!
>
> Please replace the current kojak executable in c:/TPP/bin with the 
> executable from the zip file and try running kojak again.
>
>
> Best of luck and keep us posted to your progress.
>
> -David
>
> On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:
>
>> Hi David,
>>
>> Thank you! Here are the two kojak parameter files I tested (the original 
>> and the customized).  Link: Kojak_Troubleshooting 
>> 
>>  .
>>
>> Best,
>> Zeyu 
>>
>>
>>
>>
>>
>>
>>
>> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:
>>
>> Hello Zeyu,
>>
>> Thanks for your interest in TPP and Kojak.  Yes we maintain and use Kojak 
>> in the latest release.  To help us troubleshoot this problem, would you 
>> mind sharing the parameter file used in your test?
>>
>> Thank you!
>> -David
>>
>> On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:
>>
>> Hi,
>>
>> Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the 
>> instruction and try to run a quick test. But at the very beginning, it 
>> reports an error. 
>>
>> "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann, 
>> Institute for Systems Biology Visit http://kojak-ms.org for full 
>> documentation. ** Begin Kojak Analysis ** Time at start: Fri May 24 
>> 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12 
>> preconfigured crosslinkers. Reading FASTA database: 
>> c:/TPP/data/dbase/UP05640_9606_20230222.fasta
>> ...
>>   Total Proteins: 20594
>>   Adding Kojak-generated decoys. New Total Proteins: 41188
>>   5658462 peptides to search (2785870 linkable).
>>
>> Fri May 24 02:52:45 2024 ERROR: 
>> ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt for 
>> output. Please ensure path and write permissions are correct."
>>
>> Is the error due to the output file path format? Or shall I adjust the 
>> read/write permission of the TPP?
>>
>> Best,
>> Zeyu
>>
>> -- 
>> 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 view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.com
>>  
>> 
>> .
>>
>> -- 
>> 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 view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/9f93e2d2-c59b-4ed9-8813-4728ca2e4a16n%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-05-24 Thread 'David Shteynberg' via spctools-discuss 
Hello again,

After a bit of digging I found that this is likely caused by a bug in the
current TPP compiled and distributed version of Kojak that will have to be
corrected for the next release.  Meanwhile you should be able to download
and use the official Kojak build available here:
https://kojak-ms.systemsbiology.net/download.html


This version will require additional .net dependecies!

Please replace the current kojak executable in c:/TPP/bin with the
executable from the zip file and try running kojak again.


Best of luck and keep us posted to your progress.

-David

On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:

> Hi David,
>
> Thank you! Here are the two kojak parameter files I tested (the original
> and the customized).  Link: Kojak_Troubleshooting
> 
>  .
>
> Best,
> Zeyu
>
>
>
>
>
>
>
> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:
>
> Hello Zeyu,
>
> Thanks for your interest in TPP and Kojak.  Yes we maintain and use Kojak
> in the latest release.  To help us troubleshoot this problem, would you
> mind sharing the parameter file used in your test?
>
> Thank you!
> -David
>
> On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:
>
> Hi,
>
> Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the
> instruction and try to run a quick test. But at the very beginning, it
> reports an error.
>
> "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann,
> Institute for Systems Biology Visit http://kojak-ms.org for full
> documentation. ** Begin Kojak Analysis ** Time at start: Fri May 24
> 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12
> preconfigured crosslinkers. Reading FASTA database:
> c:/TPP/data/dbase/UP05640_9606_20230222.fasta
> ...
>   Total Proteins: 20594
>   Adding Kojak-generated decoys. New Total Proteins: 41188
>   5658462 peptides to search (2785870 linkable).
>
> Fri May 24 02:52:45 2024 ERROR:
> ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt for
> output. Please ensure path and write permissions are correct."
>
> Is the error due to the output file path format? Or shall I adjust the
> read/write permission of the TPP?
>
> Best,
> Zeyu
>
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Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-05-24 Thread Zeyu Wang 
Hi David,

Thank you! Here are the two kojak parameter files I tested (the original 
and the customized).  Link: Kojak_Troubleshooting 

 .

Best,
Zeyu 







On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:

Hello Zeyu,

Thanks for your interest in TPP and Kojak.  Yes we maintain and use Kojak 
in the latest release.  To help us troubleshoot this problem, would you 
mind sharing the parameter file used in your test?

Thank you!
-David

On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:

Hi,

Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the 
instruction and try to run a quick test. But at the very beginning, it 
reports an error. 

"Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann, Institute 
for Systems Biology Visit http://kojak-ms.org for full documentation. 
** Begin Kojak Analysis ** Time at start: Fri May 24 02:52:02 2024 
Parameter file: c:/TPP/data/params/Kojak_2.conf 12 preconfigured 
crosslinkers. Reading FASTA database: 
c:/TPP/data/dbase/UP05640_9606_20230222.fasta
...
  Total Proteins: 20594
  Adding Kojak-generated decoys. New Total Proteins: 41188
  5658462 peptides to search (2785870 linkable).

Fri May 24 02:52:45 2024 ERROR: 
ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt for 
output. Please ensure path and write permissions are correct."

Is the error due to the output file path format? Or shall I adjust the 
read/write permission of the TPP?

Best,
Zeyu

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.

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Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-05-24 Thread 'David Shteynberg' via spctools-discuss 
Hello Zeyu,

Thanks for your interest in TPP and Kojak.  Yes we maintain and use Kojak
in the latest release.  To help us troubleshoot this problem, would you
mind sharing the parameter file used in your test?

Thank you!
-David

On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:

> Hi,
>
> Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the
> instruction and try to run a quick test. But at the very beginning, it
> reports an error.
>
> "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann,
> Institute for Systems Biology Visit http://kojak-ms.org for full
> documentation. ** Begin Kojak Analysis ** Time at start: Fri May 24
> 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12
> preconfigured crosslinkers. Reading FASTA database:
> c:/TPP/data/dbase/UP05640_9606_20230222.fasta
> ...
>   Total Proteins: 20594
>   Adding Kojak-generated decoys. New Total Proteins: 41188
>   5658462 peptides to search (2785870 linkable).
>
> Fri May 24 02:52:45 2024 ERROR:
> ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt for
> output. Please ensure path and write permissions are correct."
>
> Is the error due to the output file path format? Or shall I adjust the
> read/write permission of the TPP?
>
> Best,
> Zeyu
>
> --
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> "spctools-discuss" group.
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> 
> .
>

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[spctools-discuss] Issue with Kojak searching of TPP v7.0.0

2024-05-24 Thread Zeyu Wang 
Hi,

Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the 
instruction and try to run a quick test. But at the very beginning, it 
reports an error. 

"Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann, Institute 
for Systems Biology Visit http://kojak-ms.org for full documentation. 
** Begin Kojak Analysis ** Time at start: Fri May 24 02:52:02 2024 
Parameter file: c:/TPP/data/params/Kojak_2.conf 12 preconfigured 
crosslinkers. Reading FASTA database: 
c:/TPP/data/dbase/UP05640_9606_20230222.fasta
...
  Total Proteins: 20594
  Adding Kojak-generated decoys. New Total Proteins: 41188
  5658462 peptides to search (2785870 linkable).

Fri May 24 02:52:45 2024 ERROR: 
ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt for 
output. Please ensure path and write permissions are correct."

Is the error due to the output file path format? Or shall I adjust the 
read/write permission of the TPP?

Best,
Zeyu

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