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a-slide / pycoQC

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
https://a-slide.github.io/pycoQC/
GNU General Public License v3.0
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TypeError: unsupported format string passed to NoneType.__format__ #152

Open chanster-j opened 1 week ago

chanster-j commented 1 week ago

Describe the bug Hi all, I am very new the bioinformactic space and I am setout to learn how to QC nanopore data. I have managed to install pycoQC but can not get it to run sucessfully. Can someone explain what TypeError is?

TypeError: unsupported format string passed to NoneType.format

I used commend pycoQC --summary_file sequencing_summary.txt -o testing.html

Desktop (please complete the following information):

Additional context

Checking arguments values Check input data files Parse data files Merge data Cleaning data Discarding lines containing NA values 0 reads discarded Filtering out zero length reads 0 reads discarded Sorting run IDs by decreasing throughput Run-id order ['20b693e860160204aba548dd772bcb8033c74806'] Reordering runids Processing reads with Run_ID 20b693e860160204aba548dd772bcb8033c74806 / time offset: 0 Cleaning up low frequency barcodes 162 reads with low frequency barcode unset Cast value to appropriate type Reindexing dataframe by read_ids 5,063,791 Final valid reads Loading plotting interface Generating HTML report Parsing html config file Running method summary Computing plot /Users/jc/miniconda3/envs/pycoQC/lib/python3.12/site-packages/pycoQC/pycoQC_plot.py:1471: RuntimeWarning:

overflow encountered in scalar add

Traceback (most recent call last): File "/Users/jc/miniconda3/envs/pycoQC/bin/pycoQC", line 12, in sys.exit(main_pycoQC()) ^^^^^^^^^^^^^ File "/Users/jc/miniconda3/envs/pycoQC/lib/python3.12/site-packages/pycoQC/main.py", line 109, in main_pycoQC pycoQC ( File "/Users/jc/miniconda3/envs/pycoQC/lib/python3.12/site-packages/pycoQC/pycoQC.py", line 148, in pycoQC reporter.html_report( File "/Users/jc/miniconda3/envs/pycoQC/lib/python3.12/site-packages/pycoQC/pycoQC_report.py", line 84, in html_report fig = method(**method_args) ^^^^^^^^^^^^^^^^^^^^^ File "/Users/jc/miniconda3/envs/pycoQC/lib/python3.12/site-packages/pycoQC/pycoQC_plot.py", line 188, in summary lab1, dd1 = self.summary_data (df_level="all", groupby=groupby) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/jc/miniconda3/envs/pycoQC/lib/python3.12/site-packages/pycoQC/pycoQC_plot.py", line 257, in __summary_data cells.append (self.df_to_cell(df)) ^^^^^^^^^^^^^^^^^^^^^ File "/Users/jc/miniconda3/envs/pycoQC/lib/python3.12/site-packages/pycoQC/pycoQC_plot.py", line 277, in __df_to_cell l.append ("{:,.2f}".format(self._compute_N50(df["read_len"]))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: unsupported format string passed to NoneType.format

Joshtron commented 1 week ago

I am facing the same issue. It seems that newer runs don't work anymore. I am using MinKNOW 24.06.8 with Dorado 7.4.13, pycoQC v2.5.0.3 installed in a mamba environment with Python 3.12.5.