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? On Wed, Jul 29, 2020 at 9:15 AM Kate Mostovenko <kate.mostove...@gmail.com> wrote: > 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> 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> 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> >>>> 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. 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