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Nesvilab / MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
https://msfragger.nesvilab.org
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Processing interrupted, stopping MsFragger #35

Closed Golden-proteogenomics closed 5 years ago

Golden-proteogenomics commented 5 years ago

Hello, I am sorry to distrube you again about my task to search used the FragPipe.exe. The specific dataset and log files of my searching task are placed in the below link. please give me a hand in your leisure time to help me to use it. thanks again! jinshuai Sun log-fragpipe-run-at_2019-07-30_17-30-46.log CHPP_Seq.zip

chhh commented 5 years ago

Most likely causes and solutions:

I will need to see the file LysC3.mzML to investigate further.

In the meantime you can also temporarily exclude the LysC3.mzML from your analysis to see if the processing yields expected results downstream.

Golden-proteogenomics commented 5 years ago

there is a problem that the LysC3.mzML file is biger for submission of gethub limitation, Could I send it for your email?

anesvi commented 5 years ago

Not by email, please!!!!

From: Golden-proteogenomics [mailto:notifications@github.com] Sent: Tuesday, July 30, 2019 1:32 PM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [Nesvilab/MSFragger] Processing interrupted, stopping MsFragger (#35)

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there is a problem that the LysC3.mzML file is biger for submission of gethub limitation, Could I send it for your email?

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Golden-proteogenomics commented 5 years ago

if not by email, which way I can chose to transmit the file you need to you?

fcyu commented 5 years ago

@Golden-proteogenomics Could you please give me an email address so that I can share a Box folder with you? You can upload your file to the folder.

Golden-proteogenomics commented 5 years ago

email: sjsshuai@126.com

At 2019-07-31 01:53:51, "Fengchao" notifications@github.com wrote:

@Golden-proteogenomics Could you please give me an email address so that I can share a Box folder with you? You can upload your file to the folder.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

fcyu commented 5 years ago

@Golden-proteogenomics Invitation sent. Please check your email.

Golden-proteogenomics commented 5 years ago

The email sjsshuai@126.com is not error and I can receive your invitation to use BOX, However, I canont open the reasponding interlinkage, which maybe the interlinkage was off for our country, In the another hand, I try to do it in all new *.mzML files again, if I have any new probelms about this, I guess I will distrube you. thanks again.

Golden-proteogenomics commented 5 years ago

There is still a new error which is different from before when I used the new *mzML files to research again. please what can I do for this error？ log-fragpipe-run-at_2019-07-31_10-05-01.log

fcyu commented 5 years ago

@Golden-proteogenomics Your log said: Cannot find MS file at I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\GluC3.mzML

Golden-proteogenomics commented 5 years ago

Thanks, The problem why always to arise the errors was solved, whose reasons is runing three MSFragger.exe at the same times. I used the three windows to run the software in the time lead to error. Now, I have a the new problem that I want to know what modifications in my datasets can be idenficated in this tools, However, the peptide files only find some usually modifications, I don't know why this is a problem or how to find unconventional modifications.

anesvi commented 5 years ago

If you do open search, you will find peptides with mass shifts. Those are the peptides with potential modifications.

I think at this point you need to read the literature (MSFragger manuscript, other papers) on various strategies for PTM searches,

This site is for technical support.

From: Golden-proteogenomics [mailto:notifications@github.com] Sent: Wednesday, July 31, 2019 8:46 AM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/MSFragger] Processing interrupted, stopping MsFragger (#35)

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Thanks, The problem why always to arise the errors was solved, whose reasons is runing three MSFragger.exe at the same times. I used the three windows to run the software in the time lead to error. Now, I have a the new problem that I want to know what modifications in my datasets can be idenficated in this tools, However, the peptide files only find some usually modifications, I don't know why this is a problem or how to find unconventional modifications.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/MSFragger/issues/35?email_source=notifications&email_token=AIIMM667LNBMRASDLHAD22LQCGCPDA5CNFSM4IH44QR2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HD4ZY#issuecomment-516832871, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AIIMM64XAJSAJGBDUV6YF4TQCGCPDANCNFSM4IH44QRQ.

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fcyu commented 5 years ago

The open modification should be listed in the Observed Modifications column. If it is empty, could you please double check your fragger.param file?

Golden-proteogenomics commented 5 years ago

Yes, The following links are my search results. Could you valid the param which i want to set up the open-search? 1) I also want to if I want to know which and what peptides with potential modifications, I will see the peptide.tsv files or other files? 2) The modification is only have the mass shift not to give the specific modification, So, How to confirm the specific modification with the peptides?Could you give me a more detail example to tell me? fragger.zip modifications.zip peptide.zip