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 On Wednesday, 29 July 2020 17:09:03 UTC-4, Jimmy Eng wrote: > > 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 <[email protected] > <javascript:>> wrote: > >> 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]> >>> 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. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/d28a47b3-bef1-4191-af2e-fec7a0ef183do%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/d28a47b3-bef1-4191-af2e-fec7a0ef183do%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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