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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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Hi, recently i encountered an error while using SearchGui for MS/MS analysis #470

Open niks2021 opened 2 years ago

niks2021 commented 2 years ago

image please have a look at attached image ,help to solve the problem

search gui error shows:error in map loading

hbarsnes commented 2 years ago

Hi. Can you please share the SearchGUI log file? You'll find it via the Bug Report option on the Help menu.

niks2021 commented 2 years ago

21-10-2021_SearchGUI 4.1.1 log.txt

Please find attached file

hbarsnes commented 2 years ago

It seems like you are running out of memory. Please check how much memory you are allowing SearchGUI to use, try to increase it and then run SearchGUI again. You can do this via Edit > Java Settings > Memory. Note that in order to use more than 2GB of memory you would need a 64bit version of Java.

niks2021 commented 2 years ago

Thank you very much! problem get solved.

but unfortunately i stuck at another one... please give suggestions,, when i want to visvalize my results with peptide shkaer after searchGUI output ..processing gets always failed .. i am here attcahing log file also. PeptideShaker 2.2.0 log.txt

hbarsnes commented 2 years ago

It seems like it is struggling to find the following file: C:\Users\Jai\Desktop\uniprot-bovine.fmi\uniprot-bovine_concatenated_target_decoy.fmi. Does this file and (the uniprot-bovine.fmi folder) exist?

niks2021 commented 2 years ago

Hi, thank for your continuous support i really appreciate your suggestions , right now after searchGUI output when i am trying to open a project in peptide shaker and load file as searchguioutput.zip file it always shows project was not found, what can i do now?

niks2021 commented 2 years ago

It seems like it is struggling to find the following file: C:\Users\Jai\Desktop\uniprot-bovine.fmi\uniprot-bovine_concatenated_target_decoy.fmi. Does this file and (the uniprot-bovine.fmi folder) exist?

no it is not there in folder nor any such folder exist, how make .fmi files?

hbarsnes commented 2 years ago

right now after searchGUI output when i am trying to open a project in peptide shaker and load file as searchguioutput.zip file it always shows project was not found, what can i do now?

If you want to open the output from SearchGUI in PeptideShaker you need to use the New Project option. The Open Project option is for opening saved PeptideShaker projects and not for processing search results, i.e. the output from SearchGUI.

no it is not there in folder nor any such folder exist, how make .fmi files?

It should be created by the tool itself. Which is why this error message is so strange...

niks2021 commented 2 years ago

right now after searchGUI output when i am trying to open a project in peptide shaker and load file as searchguioutput.zip file it always shows project was not found, what can i do now?

If you want to open the output from SearchGUI in PeptideShaker you need to use the New Project option. The Open Project option is for opening saved PeptideShaker projects and not for processing search results, i.e. the output from SearchGUI.

no it is not there in folder nor any such folder exist, how make .fmi files?

It should be created by the tool itself. Which is why this error message is so strange...

should i run again ? or am i missing something so that error occur?

hbarsnes commented 2 years ago

You can first try using the New Project option when loading the SearchGUI zip file in PeptideShaker. If you still get the same error, then you can try rerunning the search to see if that helps.

niks2021 commented 2 years ago

You can first try using the New Project option when loading the SearchGUI zip file in PeptideShaker. If you still get the same error, then you can try rerunning the search to see if that helps.

image

i solved the .fmi error .. and load the files into peptide shaker ..but this time this was shown..

niks2021 commented 2 years ago

PeptideShaker 2.2.0 log.txt log file for your reference

hbarsnes commented 2 years ago

It seems like you have run into a known issue with the database backend in which the only known solution is to increase the amount of memory provided to PeptideShaker. You can do this via the PeptideShaker Welcome dialog > Settings & Help > Settings > Java Settings > Memory.

niks2021 commented 2 years ago

It seems like you have run into a known issue with the database backend in which the only known solution is to increase the amount of memory provided to PeptideShaker. You can do this via the PeptideShaker Welcome dialog > Settings & Help > Settings > Java Settings > Memory.

YES, i increase memory to peptide shaker and it runs smoothly thank you for your continuous support

niks2021 commented 2 years ago

PeptideShaker.log

This time i ran the file with more variable modifications like i select glycosylation along with common and fixed variables,, and peptide shaker search result get failed, can you explain the cause by seeing at attached log report, please see the report of 29th October

niks2021 commented 2 years ago

image

and what does that means system exception error

hbarsnes commented 2 years ago

A bit hard to tell from the screenshot as the resolution is a bit poor. Can you tell me which search engine is causing this error? Or perhaps provide a better screenshot? ;)

This time i ran the file with more variable modifications like i select glycosylation along with common and fixed variables,, and peptide shaker search result get failed, can you explain the cause by seeing at attached log report

Seems like one if the pep.xml files cannot be parsed. I would recommend simply skipping this search engine if that is an option?

niks2021 commented 2 years ago

image

Hi, anytime i want GOannotation,, it was twhowing this message again and again please see the pic

hbarsnes commented 2 years ago

Can you please share the PeptideShaker log file once again?

niks2021 commented 2 years ago

Please find attached file Thanks & Best Regards

NIKUNJ TYAGI PhD Scholar PROTEOMICS AND CELL BIOLOGY LAB. ANIMAL BIOTECHNOLOGY CENTRE ICAR-NDRI,KARNAL

+91-9012115198

On Tue, Nov 23, 2021 at 4:12 AM Harald Barsnes @.***> wrote:

Can you please share the PeptideShaker log file once again?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/peptide-shaker/issues/470#issuecomment-975981052, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWE3ZVRB4LFGHAD5F6MTNQDUNLBMNANCNFSM5GNNG73Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

hbarsnes commented 2 years ago

I'm afraid you cannot attach files when replying to the issues via email. Rather you have to upload them directly in the issue tracker.