Fatal Error with "Pairwise intersection and heatmap for genomic intervals" tool.

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Hi @qcsciphi

Thanks for posting the history. Very helpful.

And, I figured out what is going wrong. The tool is interpreting the input file names (the dataset name) to print out the “sample” name on the result graphic. And, if that includes any whitespace, the tool gets stuck and fails.

I’ve ticketed the enhancement to handle that better. This will happen if possible. That isn’t always true, since it depends on how the underlying tool was written. But let’s see what the developers think. Enhancement: Adjust how intervene_pairwise interprets input file names to print samples names in graphics · Issue #5997 · galaxyproject/tools-iuc · GitHub

The workaround is in the ticket but also here → Replace or remove any whitespace in the input dataset names, and remember to include in the name only what you want to later show up in the graphic. More than two files seems to be Ok too.

The “on” in the error message was the clue – it is the first word after the first whitespace in the dataset names. Whew! Bioinformatics is fun :mechanic:

Thanks for all the followup!