Issue with MiXCR Clonotyping Output and Clonotype Browser Dataset Selection

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1

Hi,

I’m working with Platforma to analyze TCR beta sequencing libraries generated using the SMARTer TCR a/b Profiling Kit v2 (with UMIs). I’m currently processing three different sets of samples.
After running the “MiXCR Clonotyping” block, I receive the message:
“Some outputs have errors”, as shown below:

screenshot
screenshot912×936 102 KB

Despite this, I see that each sample has an output report that states the analysis was completed successfully. However, when I try to proceed to the “Clonotype Browser” step (to annotate, track, and filter clonotypes), no dataset appears under “Samples & Data”, so I’m unable to continue the analysis.

I suspect the issue originates from one or more samples producing partial or malformed results during MiXCR Clonotyping, potentially preventing the creation of a complete dataset.

Here are a few specific questions I have:

  • How can I identify which sample(s) are causing the error in MiXCR Clonotyping? Are there logs or specific indicators I can check?
  • Is it possible that one problematic sample is blocking the creation of the dataset required for Clonotype Browser? (e.g., an unexpected number of input files or metadata issues)
  • Could this issue be caused by an outdated version of Platforma or any of its dependencies (e.g., Python, MiXCR version, workflow components)?
  • Finally, does the presence of UMIs require special configuration that might affect dataset compatibility?

Any suggestions or troubleshooting steps would be greatly appreciated.

Thanks in advance!

2

I am having a similar issue with Takara Smart-Seq

3

Hi guys, thank you for reporting. Could you please attach a full error message (there is a copy button top right)? Another questions:

  • are you running backend in “built-in” mode or connect to a server ?
  • which OS you use (Windows/Mac/Linux) ?

Thank you !

4

I am actually able to see 1 TCR b clonotype from 1 sample (although this sample should have 92 clonotypes) and the dataset in total should have >500 TCR clonotypes based on the MIXCR clonotyping which was run successfully. I was actually able to clear the error below (by installing the 7zip folder in the proper location) and restarted software twice but I still do not see more clonotypes loading in the browser.

PlQuickJSError: PlErrorReport: PlRunnerError:
command: /Users/mm/Platforma/local/packages/installed/platforma-open/software/platforma-open/milaboratories.software-binary-collection.software-7zip/main/1.2.0-macosx-x64.0x5B10C/bin/7zz
exit code: 127
working directory: workdirs/0x823EF
stdout:
env: /Users/mm/Platforma/local/packages/installed/platforma-open/software/platforma-open/milaboratories.software-binary-collection.software-7zip/main/1.2.0-macosx-x64.0x5B10C/bin/7zz: No such file or directory

I am using MacOS and in built in mode.

If you provide an email I can send screeshots of my MIXCR clonotyping output and clonotype browser output.

Thank you!

5

Thanks for prompt reply! Could you please share screenshots to support@milaboratories.com ? Also, are you running the most recent version of the app?