search

pinellolab / CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
Other
268 stars 92 forks source link

CRISPRessoAggregate failure #469

Open enc-kcotto opened 1 month ago

enc-kcotto commented 1 month ago

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 k.clement@utah.edu or support@edilytics.com]

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 commented 1 month ago

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 commented 1 month ago

Thanks for the quick response!

crubinstein commented 2 weeks ago

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

Colelyman commented 2 weeks ago

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