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 On Wednesday, 29 July 2020 13:58:44 UTC-4, Jimmy Eng wrote: > > 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 <[email protected] > <javascript:>> 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 <[email protected]> >>> 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 <[email protected]> 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 <[email protected]> >>>>> 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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