CRISPRessoAggregate failure

[enc-kcotto]

Describe the bug
When running the following cmd, CRISPRessoAggregate --prefix tmp/CRISPResso_on_BNL17517_additional_80k --prefix tmp/CRISPResso_on_BNL17517_additional_80k-160k --name "80k" errors out with ERROR: make_multi_report() missing 2 required positional arguments: 'crispresso_tool' and 'logger'

Expected behavior
I expected CRISPRessoAggregate to aggregate the results of the two folders specified.

To reproduce
attaching a zip of the two folders here:
crispresso_nanoporetesting.zip

Debug output
CRISPRessoAggregate --prefix tmp/CRISPResso_on_BNL17517_additional_80k --prefix tmp/CRISPResso_on_BNL17517_additional_80k-160k --name "80k" --debug

                                                                         ~~~CRISPRessoAggregate~~~                                                                             
                                                                    -Aggregation of CRISPResso Run Data-                                                                       
                                                                                                                                                                               
                                 _                                                                                                          _                                  
                                '  )                                                                                                       '  )                                
                                .-'                                 ___________________________________                                    .-'                                 
                               (____                                |      __  __  _   _  __     ___ _ |                                  (____                                
                            C)|     \                               | /\  /__ /__ |_) |_ /__  /\  | |_ |                               C)|     \                               
                              \     /                               |/--\ \_| \_| | \ |_ \_| /--\ | |_ |                                 \     /                               
                               \___/                                |__________________________________|                                  \___/                                

                                                                         [CRISPResso version 2.3.1]                                                                            

[Note that as of version 2.3.0 FLASh and Trimmomatic have been replaced by fastp for read merging and trimming. Accordingly, the --flash_command and --trimmomatic_command parameters have been replaced with --fastp_command. Also, --trimmomatic_options_string has been replaced with --fastp_options_string.

Also in version 2.3.2, when running CRISPRessoPooled in mixed-mode (amplicon file and genome are provided) the default behavior will be as if the --demultiplex_only_at_amplicons parameter is provided. This change means that reads and amplicons do not need to align to the exact locations.]
[For support contact [email protected] or [email protected]]

INFO @ Thu, 08 Aug 2024 22:12:09:
Creating Folder /home/jovyan/flbr/studies/crispresso/notebooks/CRISPRessoAggregate_on_80k

WARNING @ Thu, 08 Aug 2024 22:12:09:
Folder /home/jovyan/flbr/studies/crispresso/notebooks/CRISPRessoAggregate_on_80k already exists.

INFO @ Thu, 08 Aug 2024 22:12:09:
Read 2 folders (0 not imported)

INFO @ Thu, 08 Aug 2024 22:12:09:
Reporting summary for amplicon: "HDR"

INFO @ Thu, 08 Aug 2024 22:12:10:
All guides are equal. Performing comparison of runs for amplicon 'HDR'

WARNING @ Thu, 08 Aug 2024 22:12:10:
Plot error plot_nucleotide_quilt() missing 1 required positional argument: 'custom_colors', skipping plot

DEBUG @ Thu, 08 Aug 2024 22:12:10:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/CRISPResso2/CRISPRessoMultiProcessing.py", line 280, in run_plot
plot_func(**plot_args)
TypeError: plot_nucleotide_quilt() missing 1 required positional argument: 'custom_colors'

WARNING @ Thu, 08 Aug 2024 22:12:10:
Plot error plot_nucleotide_quilt() missing 1 required positional argument: 'custom_colors', skipping plot

DEBUG @ Thu, 08 Aug 2024 22:12:10:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/CRISPResso2/CRISPRessoMultiProcessing.py", line 280, in run_plot
plot_func(**plot_args)
TypeError: plot_nucleotide_quilt() missing 1 required positional argument: 'custom_colors'

INFO @ Thu, 08 Aug 2024 22:12:10:
Reporting summary for amplicon: "Reference"

INFO @ Thu, 08 Aug 2024 22:12:11:
All guides are equal. Performing comparison of runs for amplicon 'Reference'

WARNING @ Thu, 08 Aug 2024 22:12:11:
Plot error plot_nucleotide_quilt() missing 1 required positional argument: 'custom_colors', skipping plot

DEBUG @ Thu, 08 Aug 2024 22:12:11:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/CRISPResso2/CRISPRessoMultiProcessing.py", line 280, in run_plot
plot_func(**plot_args)
TypeError: plot_nucleotide_quilt() missing 1 required positional argument: 'custom_colors'

WARNING @ Thu, 08 Aug 2024 22:12:11:
Plot error plot_nucleotide_quilt() missing 1 required positional argument: 'custom_colors', skipping plot

DEBUG @ Thu, 08 Aug 2024 22:12:11:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/CRISPResso2/CRISPRessoMultiProcessing.py", line 280, in run_plot
plot_func(**plot_args)
TypeError: plot_nucleotide_quilt() missing 1 required positional argument: 'custom_colors'

DEBUG @ Thu, 08 Aug 2024 22:12:11:
Summarizing amplicon modifications...

DEBUG @ Thu, 08 Aug 2024 22:12:11:
Plotting reads summary...

DEBUG @ Thu, 08 Aug 2024 22:12:11:
Summarizing alignment...

Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/CRISPResso2/CRISPRessoAggregateCORE.py", line 844, in main
CRISPRessoReport.make_aggregate_report(crispresso2_info, args.name,
File "/opt/conda/lib/python3.9/site-packages/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py", line 772, in make_aggregate_report
make_multi_report(
TypeError: make_multi_report() missing 2 required positional arguments: 'crispresso_tool' and 'logger'
CRITICAL @ Thu, 08 Aug 2024 22:12:11:

ERROR: make_multi_report() missing 2 required positional arguments: 'crispresso_tool' and 'logger'

[Colelyman]

Hi @enc-kcotto,

Thanks for using CRISPResso and sorry that you are running into this error. I am working on a fix and it will be included in the next release (which should be soon)!

Thanks,
Cole

[enc-kcotto]

Thanks for the quick response!

[crubinstein]

I'm facing the same error. @enc-kcotto thanks for reporting and @Colelyman many thanks for working on this!

[Colelyman]

No problem! The new release with the fix will be out soon.