error in preprocessing

[Wojtkiewicz, Melinda]

I have been having trouble lately with a pre-processing error.  I’m new to the GUI but used it successfully a couple weeks ago but can’t seem to anymore, even with files I used before.  Attached is the log, thanks!

 

 

Melinda Wojtkiewicz

Research Coordinator

Cellular and Integrative Physiology

University of Nebraska Medical Center

9867605 Nebraska Medical Center

Omaha, NE 68198-7605

402.836.9798

 

melinda.w...@unmc.edu

 

 

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

[Joshua Klein]

Thank you for reporting the problem you've encountered.

The error(s) shown in the log unfortunately don't point to  a specific root cause inside GlycReSoft, but might be file system related. Are you storing your projects on a local hard drive or on a networked file system? If you go to the project directory and look in the `sample_dir` folder, do you see an mzML file for the sample that was being preprocessed? If it's not a local drive, please try again using the local file system and let me know the result. 

If that turns out not to be the case, I'll make a debug build with more diagnostic information.

Thank you,

Joshua Klein

--
You received this message because you are subscribed to the Google Groups "GlycReSoft" group.
To unsubscribe from this group and stop receiving emails from it, send an email to glycresoft+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/glycresoft/DM6PR05MB4236810106FB095AA6FE20639B499%40DM6PR05MB4236.namprd05.prod.outlook.com.

--

Joshua Klein

[Wojtkiewicz, Melinda]

Hi Joshua,

 

Yes, the mzML file is there:

 

 

I’ve tried reinstalling and creating new folder but that has not helped.  I don’t know if this helps you but the odd thing is when I open GlycReSoft, a windows notification pops up a that 4.12 will be installed when I close. I click yes every time but that version is also already installed… Here are screenshots:

 

 

 

 

Thank you for your help!

 

Melinda

 

From: Joshua Klein <jak...@bu.edu>
Sent: Thursday, September 15, 2022 11:48 PM
To: Wojtkiewicz, Melinda <melinda.w...@unmc.edu>
Cc: glycr...@googlegroups.com
Subject: Re: error in preprocessing

 

Non-UNMC email

To view this discussion on the web visit https://groups.google.com/d/msgid/glycresoft/DM6PR05MB4236810106FB095AA6FE20639B499%40DM6PR05MB4236.namprd05.prod.outlook.com [groups.google.com].

 

--

Joshua Klein

 

[Wojtkiewicz, Melinda]

Hi Joshua,

 

Did you have any questions or ideas for me on this?  I just wondered if I should try a full reinstall again or not….

 

Melinda

[Joshua Klein]

Please try installing the newly released version, 0.4.13, from https://www.bumc.bu.edu/msr/glycresoft/. It will collect more diagnostic information when failing to write output during deconvolution, amongst other issues that came about when I upgraded this project to Python 3. Apologies for the delay. It's been a busy few weeks and I'm not able to dedicate as much time to this project.

--

Joshua Klein

[Wojtkiewicz, Melinda]

Thanks Joshua, no need to apologize,  I totally understand you have other projects.

 

I installed the new version but still had an error.  It does seem different though, so I attached it.  Thanks again,

 

Melinda

 

From: Joshua Klein <jak...@bu.edu>
Sent: Monday, October 3, 2022 8:42 PM
To: Wojtkiewicz, Melinda <melinda.w...@unmc.edu>
Cc: glycr...@googlegroups.com
Subject: Re: error in preprocessing

 

Non-UNMC email

Please try installing the newly released version, 0. 4. 13, from https: //www. bumc. bu. edu/msr/glycresoft/ [bumc. bu. edu]. It will collect more diagnostic information when failing to write output during deconvolution, amongst other issues that came

Please try installing the newly released version, 0.4.13, from https://www.bumc.bu.edu/msr/glycresoft/ [bumc.bu.edu]. It will collect more diagnostic information when failing to write output during deconvolution, amongst other issues that came about when I upgraded this project to Python 3. Apologies for the delay. It's been a busy few weeks and I'm not able to dedicate as much time to this project.

[Joshua Klein]

Thank you, this looks like it points me in the right direction to debug what's going on. This looks like it is related to a feature I added to the mzML writing library a few months ago. I should be able to track that down pretty soon.

Thank you,

Joshua Klein

To view this discussion on the web visit https://groups.google.com/d/msgid/glycresoft/DM6PR05MB4236F387C6B3A7B4B2686A7E9B5A9%40DM6PR05MB4236.namprd05.prod.outlook.com.

--

Joshua Klein

[Joshua Klein]

I believe I've fixed the root of the problem, but I'm not able to reproduce the error you're encountering myself. I'll put out another fix on Friday, but if you can share the file you're trying to process, it would help me verify that what I'm doing makes sense. 

So far as I can tell, the problem you're encountering is the result of repeatedly trying to download a controlled vocabulary. This either means you're trying to run without an internet connection (which seems unlikely since you clearly get to the internet at least once in your log file), or something is going wrong during controlled vocabulary resolution. I've added safeguards that make that not an error that stops the program from finishing its task when that happens, but in the event that is still not a fix, I might need you to delete some files that GlycReSoft installs on your computer in the path "%APPDATA%/glycresoft/cv/"

Thank you,

Joshua Klein

--

Joshua Klein

[Joshua Klein]

I've released version 0.4.14 https://github.com/BostonUniversityCBMS/glycresoft_desktop/releases/download/v0.4.14/GlycReSoft_0.4.14.exe which contains the bug fix for controlled vocabulary term resolution that I think is the cause of the problem you are seeing. Please give it a try and let me know.

--

Joshua Klein