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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Error in running DIA_Speclib_Quant workflow #1372

Closed qingbo11 closed 10 months ago

qingbo11 commented 10 months ago

I run the DIA_Speclib_Quant workflow by submitting 28 DIA runs (in that way I would like to do a direct DIA quantification and let FragPipe to generate library after searching the 28 DIA runs against human reference proteome. It just showed the error right after I started the run. I actually upgraded my Java to Jave 21.0, so not sure how to address. Please take a look. log_2023-12-14_17-54-26.txt

Thanks,

fcyu commented 10 months ago

Did you change anything after loading the DIA_Speclib_Quant workflow? Could you upload your workflow file? You export it by clicking the "save to custom folder" button in the "workflow" tab.

Best,

Fengchao

qingbo11 commented 10 months ago

Hello Fengchao,

Thank you for your prompt . Attached please find the workflow file I have now.

Qingbo Shu, PhD

Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine, Tulane University JBJ Building, Rm 462 New Orleans, LA

Phone: 346-754-4664 Email: @.***

From: Fengchao @.> Sent: Friday, December 15, 2023 3:07 PM To: Nesvilab/FragPipe @.> Cc: Shu, Qingbo @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Error in running DIA_Speclib_Quant workflow (Issue #1372)

External Sender. Be aware of links, attachments and requests.

Did you change anything after loading the DIA_Speclib_Quant workflow? Could you upload your workflow file? You export it by clicking the "save to custom folder" button in the "workflow" tab.

Best,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1372#issuecomment-1858488461, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATKXG7TWVVXZPJYFKFRAYODYJS32XAVCNFSM6AAAAABAW7FCV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJYGQ4DQNBWGE. You are receiving this because you authored the thread.Message ID: @.***>

fcyu commented 10 months ago

It was truncated by GitHub. Could you go to https://github.com/Nesvilab/FragPipe/issues/1372 and upload there?

Best,

Fengchao

qingbo11 commented 10 months ago

image

fcyu commented 10 months ago

Could you zip your file?

Best,

Fengchao

qingbo11 commented 10 months ago

workflow.txt

qingbo11 commented 10 months ago

Hi Fengchao,

I cannot directly attach the original workflow file because here it is not supported. I then use notepad++ to open and copy/paste the content of the workflow file to a txt and shar it with you just now.

qingbo11 commented 10 months ago

workflow_DIA.zip Here is the zip file in case you need it.

fcyu commented 10 months ago

Could you do the following and try again?

Re-load DIA_Speclib_Quant workflow and do not change anything except for the database. What you have changed just made it worse.

Best,

Fengchao

qingbo11 commented 10 months ago

image Okay, before that, I would like to confirm with you that all the settings for the runs are okay. I have two groups (19 disease patients and 9 controls), and I set up them in the "experiment" abd "bioreplicate" respectively. You like me to close the software and redo this setting, reload the DIA_SpecLib_Quant workflow, then click "run" directly without change anything?

fcyu commented 10 months ago

There is no need to close the program. You just need to click "Load workflow" after selecting the DIA_SpecLib_Quant one. After that, check if the fasta file path is correct and then click "run".

Also, you need to remove all experimental groups by clicking the "clear groups" button. In the next release, we will (partially) support the experimental groups.

Best,

Fengchao

qingbo11 commented 10 months ago

Okay, I realized that I forgot to press the "Load workflow" button. My apologize. Thank you, now it is running. Cheers!

qingbo11 commented 10 months ago

Hello Fengchao,

Thank you for your help. I've been successfully running the DIA workflow. Now I got another issue for memory space limitation I believe. Please take a look at attached.

Thanks,

Qingbo Shu, PhD

Research Assistant Professor Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine, Tulane University JBJ Building, Rm 462 New Orleans, LA

Phone: 346-754-4664 Email: @.***

From: Fengchao @.> Sent: Monday, December 18, 2023 7:35 AM To: Nesvilab/FragPipe @.> Cc: Shu, Qingbo @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Error in running DIA_Speclib_Quant workflow (Issue #1372)

External Sender. Be aware of links, attachments and requests.

Closed #1372https://github.com/Nesvilab/FragPipe/issues/1372 as completed.

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1372#event-11276954781, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATKXG7WQVNP7URR7LWLBH4LYKBBCLAVCNFSM6AAAAABAW7FCV2VHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJRGI3TMOJVGQ3TQMI. You are receiving this because you authored the thread.Message ID: @.***>

fcyu commented 10 months ago

The file was discarded by GitHub. Could you go to https://github.com/Nesvilab/FragPipe/issues/1372 and upload the file there?

Thanks,

Fengchao

qingbo11 commented 10 months ago

hs_err_pid2416.log

qingbo11 commented 10 months ago

log_2023-12-20_09-54-33.txt

fcyu commented 10 months ago

It was due to the inappropriate paging file configurations. Could you change your operating system's settings according to the following screenshot? image

Best,

Fengchao

qingbo11 commented 10 months ago

Thank you, Fengchao. I changed my operating system's settings, but it turns out that I have to run the tool on another computer with better performance. Now I completed the analysis. I appreciate your help.