CrispressoBatch ERROR: unsupported operand type(s) for -: 'list' and 'int'

[nbruciaferri]

Describe the bug
Hi, any chance you guys figured out what's the problem with the CrispressoBatch? I'm getting the same error mentioned above (ERROR: unsupported operand type(s) for -: 'list' and 'int' ) and with the --debug option the error is raised at line 639 in CRISPRessoBatchCORE.py. I'm using the latest version 2.3.2.

Thanks!

Expected behavior
To run correctly.

To reproduce
CRISPResso command to reproduce the behavior.

Debug output
Paste the entire output when you run CRISPResso with the flag --debug.

[nbruciaferri]

This was also mentioned in Issue #522

[Colelyman]

Hi @nbruciaferri,

Thanks for using CRISPResso and for submitting this bug! We unfortunately have not been able to reproduce it, would you mind sharing your batch file and the command that you used to run CRISPRessoBatch? Give the line number, I anticipate that it has something to do with the sgRNAs, but we are not certain.

Also, we recently released v2.3.3, would you mind seeing if that version has the bug as well?

Thanks,
Cole

[Colelyman]

Hi @nbruciaferri,

Never mind, I was able to find a dataset that reproduced the error! And I think I have a fix for it. If you feel comfortable, could you try running this branch of CRISPResso with the fix? https://github.com/edilytics/CRISPResso2/tree/cole/fix-batch-include-idxs This will make sure that it works for your specific case (and gives you a working version before this is released).

In case you aren't familiar with how to get CRISPResso installed from this branch, here is what you can do:

1. Clone the branch https://github.com/edilytics/CRISPResso2/tree/cole/fix-batch-include-idxs
2. Activate a conda environment that had previously installed CRISPResso (this ensures that all of the dependencies are available)
3. Go to the directory where you cloned the branch and run pip install .
4. Run CRISPResso like normal

Thanks,
Cole