Mageck NEST cannot find control genes/sgRNAs

Question

[liz.b]

When I run mageck nest with the command below, I get the error that the control sgRNAs cannot be found. Does anyone know the correct format to pass the controls to mageck nest?

Command I'm running:

mageck_nest nest -k count.txt \
  -d designmatrix4.txt \
  --norm-method control \
  -e controls.txt \
  -n nest

The only time it can find the controls is if, instead of passing a file for -e, I pass a single gene name:

mageck_nest nest -k count.txt \
  -d designmatrix4.txt \
  --norm-method control \
  -e TERGENIC76054 \
  -n nest

(Which then subsequently throws a long load of python errors, and isn't the analysis I want anyway).

Any format for controls.txt that I can think of doesn't seem to work (and the demo list of controls doesn't work).

Any suggestions appreciated!

[GenoMax]

and the demo list of controls doesn't work

Are you including the names as one per line in the file?

[liz.b]

Yes, as far as I can tell.

The demo file looks like:

And my file looks like:

These formats have worked fine with MLE, but don't seem to work with NEST...

[GenoMax]

For future. Don't post screenshots of text content. You can use 101010 button in the edit window to format text as monospaced code.