Hello Organizers, The dream_runner.py script is failing for a couple reasons currently: 1) The sim3*_filtered.bedpe files do not contain a quant value and the fusionQuantificationEvaluator.py expects an 11th field. ``` File "/opt/SMC-RNA-Challenge/script/../FusionQuantification/Evaluator/fusionQuantificationEvaluator.py", line 137, in get_truth_values truth_values.append(string_to_value(truth_bedpe[x][10])) IndexError: list index out of range ``` 2) The bedpe spec described in the wiki(SMC-RNA » 2.3 - Data Description) allows a "." to be used as a quant value but the script is not equipped to handle these. Python cannot evaluate "." as a float leading to an error being thrown. Upstream scripts handle the "." correctly including bedpeValidatorS.py in the "validation" phase. ``` File "../FusionQuantification/Evaluator/fusionQuantificationEvaluator.py", line 47, in string_to_value userInput = float(message) ValueError: could not convert string to float: . ``` What is the format of the bedpe that is expected now? With or without an 11th field?   Are there any plans to get a minimal test working with the current sim data/code before challenge2 deadline?   In general, this challenge has been fraught with simple errors that prevent even the most basic of test runs to be completed successfully. Why is this? I would ask that you please run at least one example from(SMC-RNA-Examples) as part of your development process.

Created by Jeff Jasper jasper1918
Dear Jeff, Thank you for bringing these up. For now, there is not a timeline for when fusionQuantification values will be added to the bedpe files, so please kindly avoid running the `fusionQuantificationEvaluator.py` for now. I will look into the 2nd issue soon, and will make sure that there is a minimal test working with the data. Best, Thomas

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