When running CRISPRessoBatch with both guide_seq and expected_hdr_amplicon_seq, consistently getting error, ERROR: unsupported operand type(s) for -: 'list' and 'int'

[munchr-gene1]

Describe the bug
I am running CRISPRessoBatch (v2.3.3) on a set of samples using both guide_seq and expected_hdr_amplicon_seq. The individual samples process successfully, and the quantification data for each is generated correctly. However, the run crashes during the final batch comparison step ("Performing comparison of batches"). This error does not occur unless both parameters are inculded in the batch.tsv

The error is a TypeError in CRISPRessoBatchCORE.py at line 637. It appears the code attempts to subtract the sgRNA cut site integer from include_idxs, which is stored as a Python list instead of a numpy array.

Expected behavior
The software should successfully generate the batch summary plots (overlaying the quantification windows relative to the sgRNA cut site) and complete the execution without crashing.

To reproduce
Run CRISPRessoBatch using the Docker image pinellolab/crispresso2:v2.3.3.
Use a batch settings file containing amplicons that have an expected_hdr_amplicon_seq and guide_seq defined.
Include flags --place_report_in_output_folder, --debug, and --dump.

CRISPRessoBatch
-bs batch_settings.tsv
--display_name BATCH_NAME
--zip_output
--place_report_in_output_folder
--n_processes 6
--verbosity 4
--debug
--dump

Debug output
INFO @ (90.0% done):
Reporting summary for amplicon: "AMPLICON_NAME"

DEBUG @ (90.0% done):
Plotting nucleotide quilt for AMPLICON_NAME

INFO @ (93.0% done):
Reporting summary for amplicon: "AMPLICON_WITH_SGRNA"

INFO @ (93.0% done):
All guides are equal.
Performing comparison of batches for amplicon 'AMPLICON_WITH_SGRNA'

CRITICAL @ (93.0% done):
ERROR: unsupported operand type(s) for -: 'list' and 'int'

Traceback (most recent call last):
File "/opt/conda/lib/python3.12/site-packages/CRISPResso2-2.3.3-py3.12-linux-x86_64.egg/CRISPResso2/CRISPRessoBatchCORE.py", line 637, in main
sub_include_idxs = include_idxs - sgRNA_plot_idxs[0]
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
TypeError: unsupported operand type(s) for -: 'list' and 'int'

[Colelyman]

Hi @munchr-gene1,

Thanks for using CRISPResso and for filing this bug. Luckily we have a fix for this, and it will be included in the next release. If you want to use a pre-release version that has the fix you can find the Docker image at edilytics/crispresso2:v2.3.4rc3.

Please let us know if you still run into the issue in the pre-release version.

Thanks,
Cole

[petlu-netizen]

Hello, also running into this issue with CRISPResso2.3.3 (prime editing mode) in miniconda/Linux Mint - any possible fix or workaround for my implementation?

[Colelyman]

Hi @petlu-netizen,

Thank you for using CRISPResso! Have you tried the pre-release linked in my other comment? It should have the fix for Prime Editing mode as well.

Please let us know if that doesn't work, or you aren't using Docker.

Thanks,
Cole

[petlu-netizen]

Hello Cole,

thank you for reaching out so quickly.

No, I am not using Docker - I have an older laptop running Linux Mint 22.2 Cinnamon 64-bit, in which I installed Miniconda in Terminal and subsequently CRISPResso2_env. When I run it, I end up on 90% of the batch analysis and with the same error as the original poster.

Is there a workaround for my setup? I have so far managed to google that such errors might have something to do with Linux Mint, but I am very much a rookie in all things Linux, so I would prefer not to have to go through a distro change if not necessary.

Best regards,
Lucie

[Colelyman]

Hi Lucie,

Thanks for more information. You shouldn't need to change Linux distro's to get this to work. Probably the easiest way would be to try Docker and you can get the Docker image with the fix by running docker pull edilytics/crispresso2:v2.3.4rc3 and then follow the instructions of running it at https://docs.crispresso.com/installation.html#docker

If you would rather not run it via Docker, here is how you can install a version with the fix.

1. Activate the CRISPResso2_env conda environment that you already created, with something like miniconda activate CRISPResso2_env.
2. Download the version of CRISPResso with the fix, git clone https://github.com/pinellolab/CRISPResso2.git.
3. Move into that directory with cd CRISPResso2.
4. Install CRISPResso with pip install ..
5. Run CRISPResso like normal CRISPResso -r1 ....

Please let us know if you run into any issues!

Thanks,
Cole

[crubinstein]

Hi @Colelyman,

Thanks for implementing a fix for this CRISPRessoBatch problem. Also experienced a similar problem. For me, it seems to hinge specifically on inclusion of an expected HDR amplicon. I look forward to the next release!

Thanks,
Dustin