Weird package errors which results in nothing opening

[kpan028]

Hi,

I just downloaded the script last week. I used it for a couple of days and loved it but now it doesn't seem to be working anymore. I've tried everything, re-installing VC, python and reinstalling the script and the dependencies. Nothing worked. I then used conda to install everything and it seemed that all the packages were installed and working. The browser page comes on but nothing works after that. We're getting error in packages folder.

TimsPlot_script_issue.docx

[zack-kirsch]

Hi,
It looks like one of the errors that's coming through is that the StrippedSequence column is missing. What search software or file type is being used for your input? I'm wondering if there's a mismatch with software and the uploaded file or that in the Spectronaut report (if you're using Spectronaut), that the PEP.StrippedSequence column is missing.
If the app is able to launch, then your issue may not be related to any missing python libraries.

[kpan028]

Hi, It's Peaks output file, db.psm.csv. Another colleague of mine who has a mac was able to run the script and he used the same output file. Not sure what's happening. Is there anything else I can do? As I mentioned, I tried using anaconda prompt as well and even that works absolutely fine. Then it just hangs, if I try to do anything. Thanks, Kirti

…

On Mon, 18 Aug 2025 at 23:14, zack-kirsch ***@***.***> wrote: *zack-kirsch* left a comment (zack-kirsch/timsplot#1) <#1 (comment)> Hi, It looks like one of the errors that's coming through is that the StrippedSequence column is missing. What search software or file type is being used for your input? I'm wondering if there's a mismatch with software and the uploaded file or that in the Spectronaut report (if you're using Spectronaut), that the PEP.StrippedSequence column is missing. If the app is able to launch, then your issue may not be related to any missing python libraries. — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A46AVKT3MU4M2PF3T3OXDJD3OHGVHAVCNFSM6AAAAACEEGFJC2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTCOJWHAYDKMJQG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[zack-kirsch]

Hi Kirti,
How big is the file? It's possible it could be taking a bit if the file is sufficiently big for the input functions to parse through.
To clarify, you're able to launch the app and load in your file, but then it's stuck with the loading icons or you get the PEP.StrippedSequence error?

[kpan028]

Hi, It's a big file. I made changes in the metadata table and now it's working fine. I split the samples into 2 groups and now it seems to be happy. Not sure why but things look okay. [image: image.png]

…

On Tue, 19 Aug 2025 at 00:27, zack-kirsch ***@***.***> wrote: *zack-kirsch* left a comment (zack-kirsch/timsplot#1) <#1 (comment)> Hi Kirti, How big is the file? It's possible it could be taking a bit if the file is sufficiently big for the input functions to parse through. To clarify, you're able to launch the app and load in your file, but then it's stuck with the loading icons or you get the PEP.StrippedSequence error? — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A46AVKVN33GOPAFB2FIA65D3OHPGTAVCNFSM6AAAAACEEGFJC2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTCOJXGE3TAMZRGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>