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 should be able to proceed with the analysis.
I'll email the TPP developer offline to figure out if the behavior you're seeing (which I have confirmed myself here), that is writing the search results to the same directory as comet.params instead of the input mzML, is normal. It doesn't seem intuitive to me but maybe there was a change I made in Comet, which I'm currently not aware of, that's causing this. Jimmy 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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