Percolator Error in TPP

[Gabrielle H]

Hello, 

I exported a Comet search as a txt file to search with percolator and the percolator has now been "running" for three days. When I try to kill the job, it gives me "Unable to kill command 8760! ()." I'm guessing it's stuck in a loop, but I was wondering what the best way of ending job/fixing the program would be. Thank you for your help.

[Luis Mendoza]

Hello,

Is this running on your local machine?  If so, you can see if Percolator is still running by either opening the Task Manager (if on Windows) or executing the "ps" command (in Linux).

Most likely, the command might have timed out due a very long running time, and the interface (Petunia) is not aware of this.  On the command output page, you can find a button that overrides the status and marks it as "finished".

Hope this helps,

--Luis

On Mon, Jun 8, 2020 at 3:22 PM Gabrielle H <cinnamo...@gmail.com> wrote:

Hello, 

I exported a Comet search as a txt file to search with percolator and the percolator has now been "running" for three days. When I try to kill the job, it gives me "Unable to kill command 8760! ()." I'm guessing it's stuck in a loop, but I was wondering what the best way of ending job/fixing the program would be. Thank you for your help.

--
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/8eb7e6e7-42f6-4b73-b27d-50833717a4e7o%40googlegroups.com.

[Jimmy Eng]

Confirm that you are using Comet's Percolator output which you can generate by setting "output_percolatorfile = 1" in the search parameters.  This will create a tab-delimited text file with a ".pin" file extension.  Note that this is different than Comet's ".txt" output file which is a different tab-delimited output file that's not meant for Percolator.

[Gabrielle H]

Hello Luis,

Percolator is no longer running in Task Manager, so it definitely timed out. I tried to "kill job" in the command page and I keep getting the same error. Is there a way around this? Thank you for the help.

- Gabby

On Monday, June 8, 2020 at 6:36:45 PM UTC-4, Luis wrote:

Hello,

Is this running on your local machine?  If so, you can see if Percolator is still running by either opening the Task Manager (if on Windows) or executing the "ps" command (in Linux).

Most likely, the command might have timed out due a very long running time, and the interface (Petunia) is not aware of this.  On the command output page, you can find a button that overrides the status and marks it as "finished".

Hope this helps,

--Luis

On Mon, Jun 8, 2020 at 3:22 PM Gabrielle H <cinnamo...@gmail.com> wrote:

Hello, 

I exported a Comet search as a txt file to search with percolator and the percolator has now been "running" for three days. When I try to kill the job, it gives me "Unable to kill command 8760! ()." I'm guessing it's stuck in a loop, but I was wondering what the best way of ending job/fixing the program would be. Thank you for your help.

--
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...@googlegroups.com.

[Gabrielle H]

Hello Jimmy,

I have not tried that, that's probably where the problem is coming from. I will do that and get back to you. Do you know how to kill the command of the job that is currently running without getting that error? Thank you for your help!

- Gabby

[Luis Mendoza]

Hi Gabby,

So since Percolator is not actually running, it just means that the interface is confused.  On that page where you see the command list, click on "View" (instead of "Kill Job"), and at the bottom of the page that comes up you will find a small link (at the end of "If your commands have actually completed but the server timed out, click here") that will allow you to explicitly tell the interface to consider this job "finished".

Cheers,

--Luis

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/43409e48-fe23-44f7-97e3-a9a08d216a6eo%40googlegroups.com.

[Gabrielle H]

Hi Luis,

That worked, thank you so much for your help!

Best,

-Gabby

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/43409e48-fe23-44f7-97e3-a9a08d216a6eo%40googlegroups.com.

[Gabrielle H]

Hello Jimmy,

I was able to create a .pin file from Comet, but how do I run that in the external Percolator tool on TPP when it only accepts .txt files? Thank you for your help!

Best,

Gabby

On Monday, June 8, 2020 at 6:43:54 PM UTC-4, Jimmy Eng wrote: