Invalid type for the value of the key n50: <class 'NoneType'>

[ZTehrani]

Hello ToulligQC Team,

I have used Dorado to do basecalling and demultiplexing of my reads. Now to create the QC report using ToulligQC version 2.6, I first renamed the column barcode to barcode arrangement in basecalling summary file, then removed the barcoding kit name from barcodes. I am getting this error and don't understand what is causing that. Would appreciate your help

ToulligQC version 2.6

• Initialize extractors
• Start Toulligqc info extractor
• End of Toulligqc info extractor (done in 0m0.00s)
• Start Pod5 extractor
• End of Pod5 extractor (done in 0m0.04s)
• Start Basecaller sequencing summary extractor
  • Load sequencing summary file (913.38 MB used) in 1m8.76s Traceback (most recent call last): File "/usr/local/bin/toulligqc", line 8, in sys.exit(main()) ^^^^^^ File "/usr/local/lib/python3.11/site-packages/toulligqc/toulligqc.py", line 398, in main extractor.extract(result_dict) File "/usr/local/lib/python3.11/site-packages/toulligqc/sequencing_summary_extractor.py", line 223, in extract set_result_value(self, result_dict, "n50", compute_NXX(self.dataframe_dict, 50)) File "/usr/local/lib/python3.11/site-packages/toulligqc/extractor_common.py", line 39, in set_result_value _check_result_key_value(key, value) File "/usr/local/lib/python3.11/site-packages/toulligqc/extractor_common.py", line 66, in _check_result_key_value raise TypeError("Invalid type for the value of the key {}: {} ".format(key, type(value))) TypeError: Invalid type for the value of the key n50: <class 'NoneType'>

The command I ran:

toulligqc --report-name 'Sequencing Report' --sequencing-summary-source [path to basecalling summary] --pod5-source [path to pod5 files] --html-report-path report.html --data-report-path report.data --barcoding --barcodes barcode01,barcode02,barcode03,barcode04,barcode05,barcode06,barcode07,barcode08,barcode09,barcode10,barcode11,barcode12,barcode13,barcode14,barcode15,barcode16,barcode17,barcode18,barcode19,barcode20,barcode21,barcode22,barcode23,barcode24,barcode25,barcode26,barcode27,barcode28,barcode29,barcode30,barcode31,barcode32,barcode33,barcode34,barcode35,barcode36,barcode37,barcode38,barcode39,barcode40,barcode41,barcode42,barcode43,barcode44,barcode45,barcode46,barcode47,barcode48

[alihamraoui]

Hi @ZTehrani,

It seems that you're encountering the same issue as in #28. We addressed this in toulligQC v2.7.1. Please try installing the newer version.

Since it's just a compatibility issue with Pandas, you can also resolve the problem by installing pandas==2.1.4 and numpy==1.26.4 via pip.

Best regards, Ali

[alihamraoui]

As a quick tip, you can use --barcodes barcode01:barcode48 instead of listing each barcode individually from barcode01 to barcode48. 😉