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LUMC / HAMLET

RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department
MIT License
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Error: Invalid value: Unexpected column names #2

Closed moniekvanselst closed 3 years ago

moniekvanselst commented 4 years ago

While running HAMLET with a smal sample it did not find any fusions with fusioncatcher, when this happens the last column "Predicted_effect" is not made in the output. This causes plot_fc to have an "Error: Invalid value: Unexpected column names" error.

After manually adding the column name it worked again, only to give a "null division error" in intersect_fusions.

I copied both errors in the attached files plot_fc_ERROR.txt intersect_fusions_ERROR.txt

Redmar-van-den-Berg commented 4 years ago

Can you share a minimum fastq dataset (preferably) or set of inputs for fusioncatcher that can be used to replicate this issue?

moniekvanselst commented 4 years ago

The samples are still to big to be uploaded, so i put them here: https://drive.google.com/drive/folders/1icByNwdAaiTy1r5os3Fb3J6-BbULPSAN?usp=sharing

note: sample NOMO1-16714 also has the error that is descriped in issue 3

Redmar-van-den-Berg commented 4 years ago

Thanks for the data, I will have a look. Do you mind if I add the data from NOMO1-16714 to the tests data for HAMLET? That way we can make sure that these issues do not show up in later versions of HAMLET

moniekvanselst commented 4 years ago

You can use all of the samples for as test data if you want.

Redmar-van-den-Berg commented 4 years ago

This bug has been fixed upstream, I'm waiting for a new release of the tool in question to include it in HAMLET: https://github.com/bow/crimson/pull/12

Redmar-van-den-Berg commented 3 years ago

This has been fixed in the devel branch (See 9a46725)