Error while running prophets with the comet results from searchGUI

[JAVAN OKENDO]

I get the following error even though my mzML raw files are in the "Data" dir. Why is the program complaining about the .pepXML not found and yet am doing the comet search? I am stuck and I disparately need your assistance

• c:/Data/170909_CH_C1_T006_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T007_FT_R2.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T009_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T010_FT_R2.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T011_FT_R2.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T013_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T014_FT_R2.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T015_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T025_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T026_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T027_FT_R2.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T037_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T042_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T049_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T051_FT_R2.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T052_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T053_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T054_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T061_FT_R2.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T062_FT_R2.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T064_FT_R2.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T069_FT_R2.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T073_FT_R2.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T075_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T077_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T080_FT.pep.xml (file not found: not created or deleted?)
• c:/Data/170909_CH_C1_T084_FT_R2.pep.xml (file not found: not created or deleted?

[Jimmy Eng]

Javan,

This implies the Comet search has not run.  How are you attempting to running Comet?  You mention searchGUI in your title ... are you using the TPP to run Comet or CometOmic's SearchGUI?

Jimmy

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[Javan Okendo]

Hi,

 How are you attempting to running Comet?

I am running this data using the TPP program.

The program gives this message

Comet version 2018.01 rev. 4

 The comet.params file is from version 2019.01
 Please update your comet.params file.  You can generate
 a new parameters file using "comet -p"

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[JAVAN OKENDO]

The TPP is complaining about the parameter file:

Comet version 2018.01 rev. 4

 The comet.params file is from version 2019.01
 Please update your comet.params file.  You can generate
 a new parameters file using "comet -p"

I think TPP runs comet 2018.01 and my parameter file was generated using comet 2019.01

[Jimmy Eng]

Javan,

As the message states, the Comet binary is for version 2018.01 yet you are attempting to use a comet.params file for newer Comet version 2019.01.  You have 2 options.  

1. The first is to get rid of the comet.params you're using and grab one for version 2018.01.   At the top of this page, you can download example comet.params files for version 2018.01.  Rename them to just "comet.params", modify parameters as needed, and try the search again.
2. Your second option is to stick with your 2019.01 parameters file and update the Comet executable.  I would personally go this route.  To do that, go here and download the comet_2019015.zip file.  Grab the comet.2019015.win64.exe binary within that zip archive, rename it to comet.exe and place it in c:\TPP\bin\.  You will be replacing the existing 2018.01.4 version of comet.exe in that directory (which you may consider backing up before replacing).  Try the search again after updating the binary.

Good luck.

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[JAVAN OKENDO]

Hi Jimmy,

The second option works and it is the best thing to do.

Thanks,

Javan Okendo

On Monday, April 13, 2020 at 7:27:44 PM UTC+2, JAVAN OKENDO wrote:

[Kate Mostovenko]

Dear Jimmy,

I have a similar problem. I have replaced the parameter file to an older version and tried updated Comet version with the appropriate parameter file but I still get the error /190417_CytHumSt_1_Pep3D_Spectrum.pep.xml (file not found: not created or deleted?).

TPP no longer complains about the parameter file though and looks like it is going through the search but then seems to abruptly terminate the process:

Comet version "2019.01 rev. 5"

 Search start:  07/29/2020, 12:08:28 PM
 - Input file: 190417_CytHumSt_1_Pep3D_Spectrum.mzML
   - Load spectra: 1458
     - Search progress:   4%
     - Post analysis:  done
 Search end:    07/29/2020, 12:08:30 PM, 0m:2s

Is there something else I could try?

Thank you,

Kate Mostovenko

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[Jimmy Eng]

Hi Kate. Your search seems to have completed fine.  The "Search end:" text would not show up if the search terminated abruptly so I think you're seeing a different issue.  However, if you can send me your 190417_CytHumSt_1_Pep3D_Spectrum.mzML file and comet.params, I'll take a look to confirm.

I'm not sure what the issue is as Comet does seem to have completed normally (even though the 4% search progress is odd but can be explained by an odd mzML input).  Before I have a chance to see your mzML and params files, these would be my questions:

• Simple thing to check is if you have "output_pepxmlfile = 1" set in your comet.params file as Comet will not write out a pep.xml file if this parameter isn't set.
• Assuming the parameter is set correctly, if you open Windows Explorer and browse the directory where the mzML file is located, do you also see a pep.xml file in that directory?
• It would also be helpful to see the full "file not found" error message.  The full directory path before the first slash in "/190417..." is missing.  Can you confirm the directory path in the error message is correct i.e. the path where the mzML file is located?
  

[Kate Mostovenko]

Hi Jimmy,

You are right! I found the resulting pepXML files, they were written in a different folder. I have been struggling to make files save to a designated folder but I keep on getting results in the same folder with my parameter files. Hence full error:

k:/TPP/data/params/190417_CytHumSt_1_Pep3D_Spectrum.pep.xml (file not found: not created or deleted?). While my mzML files are in k:/TPP/data/SpikeMix/raw

Could that be the source for this error and can I fix it?

Thank you for your help,

Kate

[Jimmy Eng]

Kate,

Copy the k:/TPP/data/params/comet.params folder to the same folder that contains your mzML (k:/TPP/data/SpikeMix/raw/).  Then repeat your search but choose k:/TPP/data/SpikeMix/raw/comet.params as the search parameters.  This should get the pep.xml written in the same directory and you should be able to proceed with the analysis.

I'll email the TPP developer offline to figure out if the behavior you're seeing (which I have confirmed myself here), that is writing the search results to the same directory as comet.params instead of the input mzML, is normal.  It doesn't seem intuitive to me but maybe there was a change I made in Comet, which I'm currently not aware of, that's causing this.

Jimmy

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[Jimmy Eng]

Kate,

It turns out it's normal behavior for the search results to be written into the directory that contains the comet.params file.  Can you tell me what tool/process you were running that generated the "(file not found: not created or deleted?)" error message?

On Wed, Jul 29, 2020 at 1:10 PM Kate Mostovenko <kate.mo...@gmail.com> wrote:

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[Kate Mostovenko]

Hi Jimmy,

Thank you for your help. I was just running Comet search in TPP. Once I located the resulting files, there were no more problems processing further.

Just FYI, X!Tandem does similar thing with writing resulting pepXML files to the folder with parameters, I guess it is an overall TPP behavior.

Kate

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