"Uncaught exception in exposed API method:" while using bioblend to run workflow


I am trying to run a workflow from a python program and getting the error message “ConnectionError: Unexpected HTTP status code: 500: {“err_msg”: “Uncaught exception in exposed API method:”, “err_code”: 0}”. I have been able to create a history and upload a few files to the history, but when I run the workflow, I get this error message.

My workflow is:

  • Download and Extract Reads in FASTA/Q format from NCBI SRA (Galaxy Version
  • Trimmomatic (Version 0.36.2)
  • FastQC (Version 0.69)
  • HISAT2 (Version 2.1.0)
  • featureCounts (Version 1.6.2)

Any help in diagnosing this issue would be much appreciated as I am new to the bioblend library and functionality

Are you running this against a local server ? If so the server logs contain a traceback indicating why this didn’t work. Here’s an example for how to run workflows via bioblend: https://github.com/nsoranzo/bioblend-tutorial/blob/master/ex1_galaxy_api_answers.ipynb

I am not. I am trying to run using the Galaxy servers as I do not have access to a local server.

That’s ok, but then in the absence of any error messages, can you show us your code in order to debug this?