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
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,
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
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:
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.
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
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
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
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 wrote:
> I get the following error even though
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
10 matches
Mail list logo
