Description
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[Note that as of version 2.3.0 FLASh and Trimmomatic have been replaced by fastp for read merging and trimming.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'