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Nesvilab / PD-Nodes

The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes
http://www.nesvilab.org/PD-Nodes/
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PeptideProphet (Philosopher) not running with non-specific searches... #23

Closed JulBM closed 2 years ago

JulBM commented 3 years ago

Hello!

I have been trying to run MS Fragger node in PD2.5 to obtain nicer output tables at peptide level. I'm working with unspecific workflows for peptidomics. I have successfully managed to run my files using the FragPipe, using peptideProphet/philosopher. I assumed this would work fine in PD as well, but I keep getting the same error over and over, leading to 'execution failure'.

See below the reported messages (including ERRORS) since Philosopher node starts... All four options of Philosopher were set to 'true'. The error reports that no-enzyme is not an option for peptide validation. Any other solution that I could substitute this for if it's not working? Thanks a lot in advance.

Julia Bauzá-Martinez

Time Processing Node Level Message 10/29 02:52 PM Job Execution Info ----- Job execution until failure took: 19 min 10 s. ----- 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [31mFATA[0m[14:52:12] Cannot execute program. there was an error with PeptideProphet, please check your parameters and input files

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info ERROR: Unrecognized enzyme No-Enzyme - please specify enzyme with -E option

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info Unknown file type. No file loaded.D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info Unknown file type. No file loaded.D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info file 1: D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981\file.pepXML

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Executing PeptideProphet v4.0.0

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info D:\bauza001\philosopher_v4.0.0_windows_amd64\philosopher.exe" "peptideprophet --database "test_database_369target_plus_IDscombined.fasta" --accmass --combine --decoy rev --decoyprobs --expectscore --nonparam --ppm "D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981\file.pepXML" 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Done
10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Creating workspace
10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Executing Workspace v4.0.0

huiyinc commented 3 years ago

Hi Julia,

The issue is because Philosopher can't recognize the search enzyme name. The MSFragger-PD node is not expected to support unspecific enzymatic digestion workflow because this workflow often requires a large amount of computational memory. Can you please tell me how much memory you have in your computer? Thanks.

Huiyin

JulBM @.***> 於 2021年10月30日 週六 下午8:59寫道：

Hello!

I have been trying to run MS Fragger node in PD2.5 to obtain nicer output tables at peptide level. I'm working with unspecific workflows for peptidomics. I have successfully managed to run my files using the FragPipe, using peptideProphet and philosopher. I assumed this would work fine in PD as well, but I keep getting the same error over and over, leading to 'execution failure'.

See below the error messages since Philosopher node starts... All four options of Philosopher were set to 'true'. The error reports that no-enzyme is not an option for peptide validation. Any other solution that I could substitute this for if it's not working? Thanks a lot in advance.

Julia Bauzá-Martinez

Time Processing Node Level Message **10/29 02:52 PM Job Execution Info ----- Job execution until failure took: 19 min 10 s. ----- 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [31mFATA[0m[14:52:12] Cannot execute program. there was an error with PeptideProphet, please check your parameters and input files

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info ERROR: Unrecognized enzyme No-Enzyme - please specify enzyme with -E option**

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info Unknown file type. No file loaded.D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info Unknown file type. No file loaded.D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info file 1: D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981\file.pepXML

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Executing PeptideProphet v4.0.0

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info D:\bauza001\philosopher_v4.0.0_windows_amd64\philosopher.exe" "peptideprophet --database "test_database_369target_plus_IDscombined.fasta" --accmass --combine --decoy rev --decoyprobs --expectscore --nonparam --ppm "D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981\file.pepXML" 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Done 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Creating workspace 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Executing Workspace v4.0.0

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JulBM commented 3 years ago

Hi Huiyin,

Thanks for your quick reply.

I am running my searches in a 48 GB ram / 8 core computer. These run fine if I when I queue one file at a time. If >1 file is simultaneously run then they fail. I also have access to a 192 GB ram /24 core computer.

So far, MS Fragger is the only search engine capable of speeding up my searches from 200h to 1 day, so I'm really keen on using this search engine. So far, I managed to run the Target/Decoy PSM validator node from PD on the MS Fragger results. This operation however outputted 650 less peptide ID than PeptideProphet through FragPipe, of a total of ~2200 peptides.

Thanks a lot!

Julia

huiyinc commented 3 years ago

Hi Julia,

A possible solution is that I will update the enzyme name in the MSFragger parameter file and send you an update version of MSFragger-PD node. You can try if this solves the problem. Can you please give me your email address? Or you can send me an email: @.*** (my email address). Thanks.

Huiyin

JulBM @.***> 於 2021年11月1日 下午5:48 寫道：



Hi Huiyin,

Thanks for your quick reply.

I am running my searches in a 48 GB ram / 8 core computer. These run fine if I when I queue one file at a time. If >1 file is simultaneously run then they fail. I also have access to a 192 GB ram /24 core computer.

So far, MS Fragger is the only search engine capable of speeding up my searches from 200h to 1 day, so I'm really keen on using this search engine. I so far managed to run the Target/Decoy PSM validator node from PD on the MS Fragger results. This operation however outputted 650 less peptide ID than PeptideProphet through FragPipe.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/23#issuecomment-956084080, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWAYPHVQZACOYCWBL5H3UJZO6HANCNFSM5HBB5AEA . 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.

JulBM commented 3 years ago

Hi Huiyin,

That sounds great. My e-mail is @.***

Thanks for your help!

Julia

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From: chuiyin @.***> Sent: Monday, 1 November 2021, 10:41 To: Nesvilab/PD-Nodes Cc: Bauza Martinez, J. (Julia); Author Subject: Re: [Nesvilab/PD-Nodes] PeptideProphet (Philosopher) not running with non-specific searches... (Issue #23)

Hi Julia,

The issue is because Philosopher can't recognize the search enzyme name. The MSFragger-PD node is not expected to support unspecific enzymatic digestion workflow because this workflow often requires a large amount of computational memory. Can you please tell me how much memory you have in your computer? Thanks.

Huiyin

JulBM @.***> 於 2021年10月30日 L六 下午8:59Œ‘道：

Hello!

I have been trying to run MS Fragger node in PD2.5 to obtain nicer output tables at peptide level. I'm working with unspecific workflows for peptidomics. I have successfully managed to run my files using the FragPipe, using peptideProphet and philosopher. I assumed this would work fine in PD as well, but I keep getting the same error over and over, leading to 'execution failure'.

See below the error messages since Philosopher node starts... All four options of Philosopher were set to 'true'. The error reports that no-enzyme is not an option for peptide validation. Any other solution that I could substitute this for if it's not working? Thanks a lot in advance.

Julia Bauzá-Martinez

Time Processing Node Level Message **10/29 02:52 PM Job Execution Info ----- Job execution until failure took: 19 min 10 s. ----- 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [31mFATA[0m[14:52:12] Cannot execute program. there was an error with PeptideProphet, please check your parameters and input files

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info ERROR: Unrecognized enzyme No-Enzyme - please specify enzyme with -E option**

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info Unknown file type. No file loaded.D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info Unknown file type. No file loaded.D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info file 1: D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981\file.pepXML

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Executing PeptideProphet v4.0.0

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info D:\bauza001\philosopher_v4.0.0_windows_amd64\philosopher.exe" "peptideprophet --database "test_database_369target_plus_IDscombined.fasta" --accmass --combine --decoy rev --decoyprobs --expectscore --nonparam --ppm "D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981\file.pepXML" 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Done 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Creating workspace 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info [36mINFO[0m[14:52:09] Executing Workspace v4.0.0

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huiyinc commented 3 years ago

Hi Julia,

I just notice that github blocks our email addresses (possibly for the security issue). So I type my email address again: dr.chuiyin@gmail.com Thanks.

Huiyin

JulBM commented 2 years ago

Hi Huiyin,

Although we managed to get it running, I am now wondering wether it worked. Mostly, I find the following messages of concern: 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info Unknown file type. No file loaded.D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

Can I be sure my files are now filtered by 0.05 or 0.01 FDR? I just cant find a probability value in the PD ouputs, and I had already assumed they were filtered by 0.01 FDR.

Let me know what you think of this messages.

Best regards,

Julia

huiyinc commented 2 years ago

Hi Julia,

Those are just warning messages from PeptideProphet (can be ignored). They are saying that they can't find the raw files, so are trying to search for mzML instead. You may check the FDR at the 'PeptideValidator' node, where you can find the default strict and relaxed FDR of 0.01 and 0.05, respectively.

Huiyin

JulBM @.***> 於 2022年3月28日 週一 下午5:21寫道：

Hi Huiyin,

Although we managed to get it running, I am now wondering wether it worked. Mostly, I find the following messages of concern: 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info Unknown file type. No file loaded.D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

Can I be sure my files are now filtered by 0.05 or 0.01 FDR? I just cant find a probability value in the PD ouputs, and I had already assumed they were filtered by 0.01 FDR.

Let me know what you think of this messages.

Best regards,

Julia

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/23#issuecomment-1080401748, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA6XGYYG5XWNFXY6FPTVCF2XVANCNFSM5HBB5AEA . You are receiving this because you modified the open/close state.Message ID: @.***>

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

JulBM commented 2 years ago

Hi Huiyin,

Thanks for your quick answer, as always. If I understood you correctly, the Peptide validator node takes the PeptideProphet FDR as input and then outputs a filtered value? Therefore I can trust the 'high confidence' peptide label on the output, or am I wrong?

If that's the case, that's awesome! great implementation :) I was worried that it had not run but the output files in the temp folders indeed have a probability value.

I only have great words about MSFragger/Philosopher... they made my peptidomics data analysis so much faster and indeed results are way better that any other search engine I tried so far.

Cheers,

Julia

huiyinc commented 2 years ago

Hi Julia,

Yes, the PeptideValidator use the PeptideProphet probabilities as input and use them for downstream FDR filter. You can trust and use the 'high confidence' peptides/proteins for further analysis (that's also what we usually do). Please feel free to ask if you have any questions.

Huiyin

JulBM @.***> 於 2022年3月28日 週一 下午7:37寫道：

Hi Huiyin,

Thanks for your quick answer, as always. If I understood you correctly, the Peptide validator node takes the PeptideProphet FDR as input and then outputs a filtered value? Therefore I can trust the 'high confidence' peptide label on the output, or am I wrong?

If that's the case, that's awesome! great implementation :) I was worried that it had not run but the output files in the temp folders indeed have a probability value.

I only have great words about MSFragger/Philosopher... they made my peptidomics data analysis so much faster and indeed results are way better that any other search engine I tried so far.

Cheers,

Julia

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/23#issuecomment-1080542527, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA7EZABWRX7IPF5AI73VCGKXTANCNFSM5HBB5AEA . You are receiving this because you modified the open/close state.Message ID: @.***>

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

anesvi commented 2 years ago

Reminds me that we get this question often about those warnings.

Perhaps we can compile PeptideProphet in philosopher with those warnings disabled. They can be ignored. I cc Guo Ci and Felipe

Best, Alexey

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From: JulBM @.> Sent: Monday, March 28, 2022 6:20:58 PM To: Nesvilab/PD-Nodes @.> Cc: Subscribed @.***> Subject: Re: [Nesvilab/PD-Nodes] PeptideProphet (Philosopher) not running with non-specific searches... (Issue #23)

External Email - Use Caution

Hi Huiyin,

Although we managed to get it running, I am now wondering wether it worked. Mostly, I find the following messages of concern: 10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info Unknown file type. No file loaded.D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: CANNOT correct data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.mzML in msms_run_summary tag...

10/29 02:52 PM (4) Philosopher (PeptideProphet) Info WARNING: cannot open data file D:\bauza001\search\PD_MS_Fragger_LongDB\New Study\temp1981/file.raw in msms_run_summary tag... unrecognized extension .raw, trying .mzML ...

Can I be sure my files are now filtered by 0.05 or 0.01 FDR? I just cant find a probability value in the PD ouputs, and I had already assumed they were filtered by 0.01 FDR.

Let me know what you think of this messages.

Best regards,

Julia

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/PD-Nodes/issues/23#issuecomment-1080401748, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM65EWH4C3GFP4XOJNDLVCF2XVANCNFSM5HBB5AEA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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