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 <kate.mostove...@gmail.com> 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 <kate.mo...@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. > 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/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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