FragPipe ERRO[19:13:18] Cannot decode packed binary. XML syntax error on line 2076829: unexpected EOF

Hello,

While trying to run LFQ-phospho the following error was encountered: ERRO[19:13:18] Cannot decode packed binary. XML syntax error on line 2076829: unexpected EOF

I may have seen a similar error addressed here in the list of questions and it mentioned about deleting .tmp files. I searched for tmp files, only found a few (see screenshot), deleted the tmp files and tried again, but the same error occurred

It is a fairly large data set, when I tried to run it on a subset of just 16 of the samples, it seemed to run fine

Thank you as always for all of your assistance!

All the best,

Jason log_2022-09-08_21-34-31.txt tmp files

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

Sep 16 '22 14:09 jmcalist

Hello,

If I can provide any additional information related to this topic please let me know

Thanks so much!

All the best,

Jason

Sep 21 '22 14:09 jmcalist

Please contact me directly by email. We may ask you to test some things for us, but easier to do directly Alexey

From: jmcalist @.> Sent: Wednesday, September 21, 2022 10:57 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: Re: [Nesvilab/FragPipe] ERRO[19:13:18] Cannot decode packed binary. XML syntax error on line 2076829: unexpected EOF (Issue #833)

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Hello,

If I can provide any additional information related to this topic please let me know

Thanks so much!

All the best,

Jason

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/833#issuecomment-1253832851, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM67SOSRQ6WCEX6PMXXLV7MO4HANCNFSM6AAAAAAQOLTIKQ. You are receiving this because you are subscribed to this thread.Message ID: @.@.>>

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Sep 21 '22 18:09 anesvi

Yes, it’s the same issue. We need to find a way to replicate it Can you check your folder. How many files you see like

interact-S22034-Nick-60.pep.xml.tmp.a05516

PTM-Prophet seem to write tmp file, that is then supposed to be renamed interact-S22034-Nick-60.mod.pep.xml

but for some reason it does not happen.

Would you be willing to contact us directly, via email, and then with help us troubleshoot it? We may need to ask you to PTM-Shepherd binary directly (and not as part of philosopher)? Also tell us if it always happens on the same file(s), or on different files each time you run. You can rerun just from PTM-Prophet step.

Thanks Alexey

From: jmcalist @.> Sent: Friday, September 16, 2022 10:04 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: [Nesvilab/FragPipe] ERRO[19:13:18] Cannot decode packed binary. XML syntax error on line 2076829: unexpected EOF (Issue #833)

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Hello,

While trying to run LFQ-phospho the following error was encountered: ERRO[19:13:18] Cannot decode packed binary. XML syntax error on line 2076829: unexpected EOF

I may have seen a similar error addressed here in the list of questions and it mentioned about deleting .tmp files. I searched for tmp files, only found a few (see screenshot), deleted the tmp files and tried again, but the same error occurred

It is a fairly large data set, when I tried to run it on a subset of just 16 of the samples, it seemed to run fine

Thank you as always for all of your assistance!

All the best,

Jason log_2022-09-08_21-34-31.txthttps://github.com/Nesvilab/FragPipe/files/9584694/log_2022-09-08_21-34-31.txt [tmp files]https://user-images.githubusercontent.com/72038445/190657539-8576e5a5-ee7d-4477-8e99-c64a8d203d65.png

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/833, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM63YCC462IHWQ7CNLDDV6R45VANCNFSM6AAAAAAQOLTIKQ. You are receiving this because you are subscribed to this thread.Message ID: @.@.>>

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Oct 11 '22 08:10 anesvi

Hi Alexey,

Thank you so much for continuing to follow up on this, we really appreciate it!

Based on your information regarding conversion of .tmp files to .mod, I noted the following in log files. In the example below, it appears that writing of the mod file for sample 9 files (highlighted in yellow below), but this error is not seen for the next sample 58. I searched two log files for mod.pep.xml" failed: Operation not permitted, and in one run this error occurred for all samples except 5 (n=63 total files), and for the other run the error occurred for all samples except 2. In both runs the error did not occur on sample 49. I am not sure if this is helpful, but just something I noticed. I would be happy to help try troubleshooting on my side, feel free to have a member of your team contact me.

PtmProphet [Work dir: C:\Users\Administrator\Desktop\Danve_phopho_all\S22034-Nick-9] C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe ptmprophet --keepold --static --em 1 --nions b --mods STY:79.966331,M:15.9949 --minprob 0.5 --maxthreads 7 interact-S22034-Nick-9.pep.xml INFO[05:40:05] Executing PTMProphet v4.4.0 INFO: Writing file interact-S22034-Nick-9.pep.xml.tmp.a00892 ...

Creating 7 threads Wait for threads to finish ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Using statically set 15 PPM tolerance ... INFO: processed 91000/91302 spectrum_queries INFO: done ... INFO: Computing EM Models ... Iterating PTM Model: ....5..done INFO: done ... INFO: done ...

Creating 7 threads Wait for threads to finish ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: Reading file interact-S22034-Nick-9.pep.xml ... INFO: written 91000/91302 spectrum_queries INFO: done ... INFO: Writing file interact-S22034-Nick-9.mod.pep.xml ... 'chmod' is not recognized as an internal or external command, operable program or batch file. INFO: done ...

command "chmod 664 interact-S22034-Nick-9.mod.pep.xml" failed: Operation not permitted INFO[05:41:37] Done Process 'PtmProphet' finished, exit code: 0 PtmProphet [Work dir: C:\Users\Administrator\Desktop\Danve_phopho_all\S22034-Nick-58] C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe ptmprophet --keepold --static --em 1 --nions b --mods STY:79.966331,M:15.9949 --minprob 0.5 --maxthreads 7 interact-S22034-Nick-58.pep.xml INFO[05:41:37] Executing PTMProphet v4.4.0 INFO: Writing file interact-S22034-Nick-58.pep.xml.tmp.a06372 ...

Creating 7 threads Wait for threads to finish ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Using statically set 15 PPM tolerance ... INFO: processed 88000/89609 spectrum_queries INFO: done ... INFO: Computing EM Models ... Iterating PTM Model: ....5..done INFO: done ... INFO: done ...

Creating 7 threads Wait for threads to finish ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: Reading file interact-S22034-Nick-58.pep.xml ... INFO: written 37000/89609 spectrum_queries INFO[05:42:48] Done Process 'PtmProphet' finished, exit code: 0

From: Alexey Nesvizhskii @.> Sent: Tuesday, October 11, 2022 4:53 AM To: Nesvilab/FragPipe @.> Cc: Jason Mcalister @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] ERRO[19:13:18] Cannot decode packed binary. XML syntax error on line 2076829: unexpected EOF (Issue #833)

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Yes, it’s the same issue. We need to find a way to replicate it Can you check your folder. How many files you see like

interact-S22034-Nick-60.pep.xml.tmp.a05516

PTM-Prophet seem to write tmp file, that is then supposed to be renamed interact-S22034-Nick-60.mod.pep.xml

but for some reason it does not happen.

Would you be willing to contact us directly, via email, and then with help us troubleshoot it? We may need to ask you to PTM-Shepherd binary directly (and not as part of philosopher)? Also tell us if it always happens on the same file(s), or on different files each time you run. You can rerun just from PTM-Prophet step.

Thanks Alexey

From: jmcalist @.> Sent: Friday, September 16, 2022 10:04 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: [Nesvilab/FragPipe] ERRO[19:13:18] Cannot decode packed binary. XML syntax error on line 2076829: unexpected EOF (Issue #833)

External Email - Use Caution

Hello,

While trying to run LFQ-phospho the following error was encountered: ERRO[19:13:18] Cannot decode packed binary. XML syntax error on line 2076829: unexpected EOF

I may have seen a similar error addressed here in the list of questions and it mentioned about deleting .tmp files. I searched for tmp files, only found a few (see screenshot), deleted the tmp files and tried again, but the same error occurred

It is a fairly large data set, when I tried to run it on a subset of just 16 of the samples, it seemed to run fine

Thank you as always for all of your assistance!

All the best,

Jason log_2022-09-08_21-34-31.txthttps://github.com/Nesvilab/FragPipe/files/9584694/log_2022-09-08_21-34-31.txt [tmp files]https://user-images.githubusercontent.com/72038445/190657539-8576e5a5-ee7d-4477-8e99-c64a8d203d65.png

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/833, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM63YCC462IHWQ7CNLDDV6R45VANCNFSM6AAAAAAQOLTIKQ. You are receiving this because you are subscribed to this thread.Message ID: @.@.>>

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Oct 11 '22 15:10 jmcalist

Dear Jason,

We were able to fix the problem in PTMProphet! Or so we hope. Felipe, could you please send Jason a pre-release of philosopher (.exe) so he can test.

Thanks Alexey

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From: jmcalist @.> Sent: Tuesday, October 11, 2022 11:47:59 AM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Comment @.> Subject: Re: [Nesvilab/FragPipe] ERRO[19:13:18] Cannot decode packed binary. XML syntax error on line 2076829: unexpected EOF (Issue #833)