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Published 20 hours ago • verified publisher icon Nesvilab

LFQ-phospho workflow: cannot decode packed binary

Open without1102 opened this issue 1 year ago • 7 comments

I tried to use LFQ-phopho workflow to quantify my phosphoproteomics data. I converted the raw files into mzML files, and run the workflow in FragPipe (v 18.0). However, it showed that "panic: Cannot decode packed binary. XML syntax error on line 408092: unexpected EOF" in search log and stopped running FragPipe. I attached my search log as below. Please help me check the log. Thank you very much.

Best,

Chuan-Chih

log_2022-09-13_16-57-14.txt

without1102 avatar Sep 13 '22 09:09 without1102

This normally means you have a temporary interact pepXML file from a previous PeptideProphet run that needs to be deleted. Please check to see if you have something that looks like a temporary xml file in your directory, delete it, and rerun the tools that have no finished.

For example: 111835_ABA200_60min_2_DDA_A227_220907.pep.xml.tmp.a12244.

Alternatively, restart your analysis in a clean directory.

On Sep 13, 2022, at 12:09, without1102 @.***> wrote:

 I tried to use LFQ-phopho workflow to quantify my phosphoproteomics data. I converted the raw files into mzML files, and run the workflow in FragPipe (v 18.0). However, it showed that "panic: Cannot decode packed binary. XML syntax error on line 408092: unexpected EOF" in search log and stopped running FragPipe. I attached my search log as below. Please help me check the log. Thank you very much.

Best,

Chuan-Chih

log_2022-09-13_16-57-14.txt

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danielgeiszler avatar Sep 13 '22 10:09 danielgeiszler

It may also happen if PTM-prophet did not complete an analysis of a fine. Can you rerun as Danny suggested, and send us the log file if still a problem

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From: danielgeiszler @.> Sent: Tuesday, September 13, 2022 6:11:32 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: Re: [Nesvilab/FragPipe] LFQ-phospho workflow: cannot decode packed binary (Issue #825)

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This normally means you have a temporary interact pepXML file from a previous PeptideProphet run that needs to be deleted. Please check to see if you have something that looks like a temporary xml file in your directory, delete it, and rerun the tools that have no finished.

Alternatively, restart your analysis in a clean directory.

On Sep 13, 2022, at 12:09, without1102 @.***> wrote:

 I tried to use LFQ-phopho workflow to quantify my phosphoproteomics data. I converted the raw files into mzML files, and run the workflow in FragPipe (v 18.0). However, it showed that "panic: Cannot decode packed binary. XML syntax error on line 408092: unexpected EOF" in search log and stopped running FragPipe. I attached my search log as below. Please help me check the log. Thank you very much.

Best,

Chuan-Chih

log_2022-09-13_16-57-14.txt

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anesvi avatar Sep 13 '22 10:09 anesvi

Hello Danny and Alexey,

Thank you for your suggestion. I deleted the temporary xml files from my previous run and rerun it. But I still got the same error message and I attached the log file. Please help me take a look. Thank you for your time.

Chuan-Chih log_2022-09-14_11-52-42.txt

without1102 avatar Sep 14 '22 04:09 without1102

It looks like fir a very small number of users PTM-Prophet has issues. Unfortunately, we do not know how to resolve this. The only thing I can suggest to try is to reduce the number of threads (set to say 8 in the Workflow tab). You can also contact us directly, if you are willing to help us debug the issue. We would need to ask you to run PTM-Prophet binary directly, not as part of Philosopher. So it is easier if you talk to us directly than via github

Best Alexey

From: without1102 @.> Sent: Wednesday, September 14, 2022 12:08 AM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Comment @.> Subject: Re: [Nesvilab/FragPipe] LFQ-phospho workflow: cannot decode packed binary (Issue #825)

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Hello Danny and Alexey,

Thank you for your suggestion. I deleted the temporary xml files from my previous run and rerun it. But I still got the same error message and I attached the log file. Please help me take a look. Thank you for your time.

Chuan-Chih log_2022-09-14_11-52-42.txthttps://github.com/Nesvilab/FragPipe/files/9562563/log_2022-09-14_11-52-42.txt

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anesvi avatar Sep 14 '22 17:09 anesvi

Dear Alexey,

I reduced the number of threads to 4, but I still got the same error. Yes, I am willing to work with you to debug this issue. Please tell me how to contact your group. Thanks.

Best,

Chuan-Chih

without1102 avatar Sep 21 '22 09:09 without1102

Please contact me at nesvi at med.umich.edu And we will communicate directly

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From: without1102 @.> Sent: Wednesday, September 21, 2022 5:27:46 AM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Comment @.> Subject: Re: [Nesvilab/FragPipe] LFQ-phospho workflow: cannot decode packed binary (Issue #825)

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Dear Alexey,

I reduced the number of threads to 4, but I still got the same error. Yes, I am willing to work with you to debug this issue. Please tell me how to contact your group. Thanks.

Best,

Chuan-Chih

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anesvi avatar Sep 21 '22 10:09 anesvi

Email me at nesvi at med.umich.edu

From: without1102 @.> Sent: Wednesday, September 21, 2022 5:28 AM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Comment @.> Subject: Re: [Nesvilab/FragPipe] LFQ-phospho workflow: cannot decode packed binary (Issue #825)

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Dear Alexey,

I reduced the number of threads to 4, but I still got the same error. Yes, I am willing to work with you to debug this issue. Please tell me how to contact your group. Thanks.

Best,

Chuan-Chih

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/825#issuecomment-1253444430, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM6675CCAZ3FR3PNDU3LV7LIJFANCNFSM6AAAAAAQLHIRUE. You are receiving this because you commented.Message ID: @.@.>>

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anesvi avatar Oct 11 '22 08:10 anesvi

We have the pre-release versions of FragPipe and MSFragger than fixes the multi-threading issue in PTMProphet.

Please contact us for the pre-release versions if you want to have a try.

Best,

Fengchao

fcyu avatar Oct 27 '22 21:10 fcyu