Issue with toulligqc_demo_data

[glustein]

Hi GenomiqueENS/toulligQC team.

I tried to run the provided sample data with toulligQC but a get the following error: ❯ toulligqc \ --report-name toulligqc_demo_aata \ --barcoding \ --barcodes BC01,BC02,BC03,BC04,BC05,B0C7 \ --telemetry-source sequencing_telemetry.js \ --sequencing-summary-source sequencing_summary.txt \ --sequencing-summary-source barcoding_summary_pass.txt \ --sequencing-summary-source barcoding_summary_fail.txt \ --output-directory output output/toulligqc_demo_aata/report.html ToulligQC version 2.2.1

• Initialize extractors
• Start Toulligqc info extractor
• End of Toulligqc info extractor (done in 0m0.00s)
• Start Sequencing telemetry extractor
• End of Sequencing telemetry extractor (done in 0m0.05s)
• Start Basecaller sequencing summary extractor Traceback (most recent call last): File "/home/glustein/.local/bin/toulligqc", line 8, in sys.exit(main()) File "/home/glustein/.local/lib/python3.10/site-packages/toulligqc/toulligqc.py", line 342, in main extractor.init() File "/home/glustein/.local/lib/python3.10/site-packages/toulligqc/sequencing_summary_extractor.py", line 116, in init self.dataframe_1d['barcode_arrangement'].cat.add_categories([0, 'other barcodes', 'passes_filtering'], File "/home/glustein/.local/lib/python3.10/site-packages/pandas/core/generic.py", line 5575, in getattr return object.getattribute(self, name) File "/home/glustein/.local/lib/python3.10/site-packages/pandas/core/accessor.py", line 182, in get accessor_obj = self._accessor(obj) File "/home/glustein/.local/lib/python3.10/site-packages/pandas/core/arrays/categorical.py", line 2717, in init self._validate(data) File "/home/glustein/.local/lib/python3.10/site-packages/pandas/core/arrays/categorical.py", line 2726, in _validate raise AttributeError("Can only use .cat accessor with a 'category' dtype") AttributeError: Can only use .cat accessor with a 'category' dtype. Did you mean: 'at'?

I don´t understand what is happening. Could you help me to solve this trouble?

Thanks

[jourdren]

Dear @glustein,

Thanks for reporting this issue.

This issue occurs when multiple sequencing summary barcode files are available like in the example dataset. If you only have one sequencing summary file, ToulligQC will work fine. I've just fixed the issue with commit 238062472f5860a8a02b96968a2058c5808fa292.

I've forgotten to add the example dataset to the list of datasets for our functional tests. Now all new ToulligQC version will always work with the exanple dataset.

A new bugfix version of ToulligQC will be published tomorrow.

Best,

Laurent.

[jourdren]

A new release of ToulligQC (2.2.2) that fix the issue has been published.