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
On Monday, 13 April 2020 14:31:47 UTC-4, Jimmy Eng wrote:
>
> 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
> <http://comet-ms.sourceforge.net/parameters/parameters_201801/>, 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
> <https://sourceforge.net/projects/comet-ms/files/>. 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.
>
> On Mon, Apr 13, 2020 at 11:18 AM Javan Okendo <javan...@gmail.com
> <javascript:>> wrote:
>
>> 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"
>>
>>
>>
>>
>> On Mon, Apr 13, 2020 at 7:40 PM Jimmy Eng <jke...@gmail.com <javascript:>>
>> wrote:
>>
>>> 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
>>>
>>> On Mon, Apr 13, 2020 at 10:27 AM JAVAN OKENDO <javan...@gmail.com
>>> <javascript:>> wrote:
>>>
>>>> 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?
>>>>
>>>> --
>>>> 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 <javascript:>.
>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/spctools-discuss/aa0607da-e037-4a8c-a94f-4bbfb5eab0e8%40googlegroups.com
>>>>
>>>> <https://groups.google.com/d/msgid/spctools-discuss/aa0607da-e037-4a8c-a94f-4bbfb5eab0e8%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>> --
>>> 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 <javascript:>.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EPk%3DzDb1yZPzAXMoDSCwH7mtNYWeMRiiy66R-A6j3Zx3Q%40mail.gmail.com
>>>
>>> <https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EPk%3DzDb1yZPzAXMoDSCwH7mtNYWeMRiiy66R-A6j3Zx3Q%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
>> 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 <javascript:>.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/spctools-discuss/CAGdnHmveXWFvWgk7v6tsEE7j9UJLxuOphNtV%2BkVmy1f8HKxN8w%40mail.gmail.com
>>
>> <https://groups.google.com/d/msgid/spctools-discuss/CAGdnHmveXWFvWgk7v6tsEE7j9UJLxuOphNtV%2BkVmy1f8HKxN8w%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
>>
>
--
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.
To view this discussion on the web visit
https://groups.google.com/d/msgid/spctools-discuss/985ddfa0-d995-47c6-8c7c-c99e8ac5defdo%40googlegroups.com.
