MSFragger Error Using PD Node

jadowell commented 1 year ago

Hi,

I running the MSFragger node through PD2.5 (with the PD2.5-dll). I am getting the following error: PD_MSFragger_Error.docx

Any ideas on what might be going on? Searching this .raw file via MSFragger in FragPipe works just fine, so it seems to something with the MSFragger node within PD.

Thanks, James

huiyinc commented 1 year ago

Hi James,

Can you please send me the MagellanServer.log file? You may find it in: C:\ProgramData\Thermo\Proteome Discoverer 2.5\Logs. Thanks.

Huiyin

jadowell @.***> 於 2023年4月7日下午9:44 寫道：

Hi,

I running the MSFragger node through PD2.5 (with the PD2.5-dll). I am getting the following error: PD_MSFragger_Error.docx https://github.com/Nesvilab/PD-Nodes/files/11179279/PD_MSFragger_Error.docx

Any ideas on what might be going on? Searching this .raw file via MSFragger in FragPipe works just fine, so it seems to something with the MSFragger node within PD.

Thanks, James

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jadowell commented 1 year ago

Hi Huiyin,

Thanks for the quick response!

I have attached the thermo.magellan.server.nlog as a text file. I'm not sure if this is the right file and/or file format. If it isn't, I am happy to dig deeper.

Thanks, James thermo.magellan.server..txt

huiyinc commented 1 year ago

Hi James,

Thanks for the help. However, this is the file for magellan server and the MagellanServer.log file should be at: C:\ProgramData\Thermo\Proteome Discoverer 2.5\Logs\MagellanServer.log. If you can't find it, maybe you can send me the logs in the Job Queue of PD v2.5.

Best,

Huiyin

jadowell @.***> 於 2023年4月10日下午9:52 寫道：

Hi Huiyin,

Thanks for the quick response!

I have attached the thermo.magellan.server.nlog as a text file. I'm not sure if this is the right file and/or file format. If it isn't, I am happy to dig deeper.

Thanks, James thermo.magellan.server..txt https://github.com/Nesvilab/PD-Nodes/files/11190864/thermo.magellan.server.txt

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jadowell commented 1 year ago

Hi Huiyin,

I think I found the right file (it was in a hidden folder on the C: drive).

Thanks, James

From: chuiyin @.> Sent: Monday, April 10, 2023 9:22 PM To: Nesvilab/PD-Nodes @.> Cc: JAMES A DOWELL @.>; Author @.> Subject: Re: [Nesvilab/PD-Nodes] MSFragger Error Using PD Node (Issue #33)

Hi James,

Thanks for the help. However, this is the file for magellan server and the MagellanServer.log file should be at: C:\ProgramData\Thermo\Proteome Discoverer 2.5\Logs\MagellanServer.log. If you can't find it, maybe you can send me the logs in the Job Queue of PD v2.5.

Best,

Huiyin

jadowell @.***> 於 2023年4月10日下午9:52 寫道：

Hi Huiyin,

Thanks for the quick response!

I have attached the thermo.magellan.server.nlog as a text file. I'm not sure if this is the right file and/or file format. If it isn't, I am happy to dig deeper.

Thanks, James thermo.magellan.server..txt https://github.com/Nesvilab/PD-Nodes/files/11190864/thermo.magellan.server.txt

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huiyinc commented 1 year ago

Hi James,

I didn't see any attachment. Can you please send it again? Thanks.

Huiyin

jadowell @.***> 於 2023年4月11日下午11:14 寫道：

Hi Huiyin,

I think I found the right file (it was in a hidden folder on the C: drive).

Thanks, James

From: chuiyin @.> Sent: Monday, April 10, 2023 9:22 PM To: Nesvilab/PD-Nodes @.> Cc: JAMES A DOWELL @.>; Author @.> Subject: Re: [Nesvilab/PD-Nodes] MSFragger Error Using PD Node (Issue #33)

Hi James,

Thanks for the help. However, this is the file for magellan server and the MagellanServer.log file should be at: C:\ProgramData\Thermo\Proteome Discoverer 2.5\Logs\MagellanServer.log. If you can't find it, maybe you can send me the logs in the Job Queue of PD v2.5.

Best,

Huiyin

jadowell @.***> 於 2023年4月10日下午9:52 寫道：

Hi Huiyin,

Thanks for the quick response!

I have attached the thermo.magellan.server.nlog as a text file. I'm not sure if this is the right file and/or file format. If it isn't, I am happy to dig deeper.

Thanks, James thermo.magellan.server..txt < https://github.com/Nesvilab/PD-Nodes/files/11190864/thermo.magellan.server.txt>

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jadowell commented 1 year ago

MagellanServer.log

Here it is. I attached it to the email but obviously it didn't pass through to GitHub.

Thanks, James

huiyinc commented 1 year ago

Hi James,

Thanks for the help. But there is no logs about you running the PD node and thus I don't know what happen when you run the MSFragger-PD node. Can you please run the MSFragger-PD node and send me the log file? Thanks.

Huiyin

jadowell @.***> 於 2023年4月12日週三下午9:11寫道：

MagellanServer.log https://github.com/Nesvilab/PD-Nodes/files/11211731/MagellanServer.log

Here it is. I attached it to the email but obviously it didn't pass through to GitHub.

Thanks, James

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

jadowell commented 1 year ago

MagellanServer.log MagellanServerError.log

Hi Huiyin,

I apologize for all the confusion. I have attached the MagellanServer log and error log that are associate with the MSFragger node. Once again, if these files are not the right ones, please email me.

Thanks, James

huiyinc commented 1 year ago

Hi James,

I have checked the log file, and here are the error messages from MSFragger-PD node:

2023-04-06 15:19:28,493 INFO [32] MSFragger - (2-5) Invalid maximum heap size: -Xmx41G 2023-04-06 15:19:28,493 INFO [32] MSFragger - (2-5) The specified size exceeds the maximum representable size. 2023-04-06 15:19:28,503 INFO [32] MSFragger - (2-5) Error: Could not create the Java Virtual Machine. 2023-04-06 15:19:28,503 INFO [32] MSFragger - (2-5) Error: A fatal exception has occurred. Program will exit.

It seems that you have JRE (32 bit) installed in the computer, instead of the JRE (64 bit), so the MSFragger-node can't be executed. One possible explanation for you being able to run MSFragger via FragPipe is that the memory usage is fewer than 2GB. Can you please check which JRE version you are using? Thanks.

Huiyin

jadowell @.***> 於 2023年4月14日週五上午2:22寫道：

MagellanServer.log https://github.com/Nesvilab/PD-Nodes/files/11225310/MagellanServer.log MagellanServerError.log https://github.com/Nesvilab/PD-Nodes/files/11225311/MagellanServerError.log

Hi Huiyin,

I apologize for all the confusion. I have attached the MagellanServer log and error log that are associate with the MSFragger node. Once again, if these files are not the right ones, please email me.

Thanks, James

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

jadowell commented 1 year ago

Hi Huiyin,

I uninstalled 32 bit JRE and installed 64 bit JRE, but I'm still getting the same error. I ran the search on the recommended test data provided on the PD node instruction page using the standard Percolator Processing/Consensus workflows. MagellanServer.log.0_.txt

Thanks, James

huiyinc commented 1 year ago

Hi James,

Here are the error messages from your log file:

2023-04-14 09:48:36,892 INFO [36] MSFragger - (16-4) Exception in thread "main" java.lang.UnsupportedClassVersionError: edu/umich/andykong/msfragger/MSFragger has been compiled by a more recent version of the Java Runtime (class file version 53.0), this version of the Java Runtime only recognizes class file versions up to 52.0 2023-04-14 09:48:36,892 INFO [36] MSFragger - (16-4) at java.lang.ClassLoader.defineClass1(Native Method) 2023-04-14 09:48:36,892 INFO [36] MSFragger - (16-4) at java.lang.ClassLoader.defineClass(Unknown Source) 2023-04-14 09:48:36,905 INFO [36] MSFragger - (16-4) at java.security.SecureClassLoader.defineClass(Unknown Source) 2023-04-14 09:48:36,905 INFO [36] MSFragger - (16-4) at java.net.URLClassLoader.defineClass(Unknown Source) 2023-04-14 09:48:36,905 INFO [36] MSFragger - (16-4) at java.net.URLClassLoader.access$100(Unknown Source) 2023-04-14 09:48:36,905 INFO [36] MSFragger - (16-4) at java.net.URLClassLoader$1.run(Unknown Source) 2023-04-14 09:48:36,920 INFO [36] MSFragger - (16-4) at java.net.URLClassLoader$1.run(Unknown Source) 2023-04-14 09:48:36,920 INFO [36] MSFragger - (16-4) at java.security.AccessController.doPrivileged(Native Method) 2023-04-14 09:48:36,920 INFO [36] MSFragger - (16-4) at java.net.URLClassLoader.findClass(Unknown Source) 2023-04-14 09:48:36,920 INFO [36] MSFragger - (16-4) at java.lang.ClassLoader.loadClass(Unknown Source) 2023-04-14 09:48:36,920 INFO [36] MSFragger - (16-4) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) 2023-04-14 09:48:36,938 INFO [36] MSFragger - (16-4) at java.lang.ClassLoader.loadClass(Unknown Source) 2023-04-14 09:48:36,938 INFO [36] MSFragger - (16-4) at sun.launcher.LauncherHelper.checkAndLoadMain(Unknown Source)

It seems you have an older version of JRE installed in the computer, and MSFragger is complied by a more recent version. Which JRE version do you install?

Best,

Huiyin

jadowell @.***> 於 2023年4月14日下午11:36 寫道：

Hi Huiyin,

I uninstalled 32 bit JRE and installed 64 bit JRE, but I'm still getting the same error. I ran the search on the recommended test data provided on the PD node instruction page using the standard Percolator Processing/Consensus workflows. MagellanServer.log.0.txt <https://github.com/Nesvilab/PD-Nodes/files/11234492/MagellanServer.log.0.txt>

Thanks, James

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jadowell commented 1 year ago

Hi Huiyin,

I resolved the issue by compiling FragPipe/MSFragger with the 64-bit developers JRE. I had originally downloaded the Frag-Pipe-jre-19.1 file from the Frag-Pipe download/installation page. This download includes the 32-bit JRE which does not seem to be compatible with the MSFragger PD node. I just wanted to clarify this for anyone who might be looking at this thread in the future.

Thanks again for all your help! -James

huiyinc commented 1 year ago

Hi James,

No problem at all, and thanks for sharing the jar file information. We will discuss it internally.

Best,

Huiyin

jadowell @.***> 於 2023年4月19日上午12:20 寫道：

Hi Huiyin,

I resolved the issue by compiling FragPipe/MSFragger with the 64-bit developers JRE. I had originally downloaded the Frag-Pipe-jre-19.1 file from the Frag-Pipe download/installation page. This download includes the 32-bit JRE which does not seem to be compatible with the MSFragger PD node. I just wanted to clarify this for anyone who might be looking at this thread in the future.

Thanks again for all your help! -James

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Nesvilab / PD-Nodes

MSFragger Error Using PD Node #33