DAY-EC activated.
DAY-EC activated.
=== repo ===
/fsx/analysis_results/ubuntu/ccv20260529r17_ont_run_qc/daylily-omics-analysis
=== run context ===
RUNID	PLATFORM	RUN_DIR	SOURCE_S3_URI	MOUNT_ID	SAMPLE_SHEET	BASECALLING_STATE	RUN_STATUS	OUTPUT_ROOT	REGION	PROFILE
20260513_ONT_HG003	ONT	/fsx/run_dir_mounts/20260513_ONT_HG003/	s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/pca100/2026/20260513_ONT_HG003/	20260513_ONT_HG003		pod5	complete	results/runs/20260513_ONT_HG003	us-west-2	lsmc
=== summary list ===
1 results/runs/20260513_ONT_HG003/run_qc/ont/tables/sequencing_summary_files.txt
/fsx/run_dir_mounts/20260513_ONT_HG003/HG003/20260513_2149_1D_PBM13745_5a9ea63e/sequencing_summary_PBM13745_5a9ea63e_ee86bd52.txt
=== pycoqc log ===
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/bin/pycoQC
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/lib/python3.13/site-packages/pycoQC/__main__.py:11: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import resource_filename
Checking arguments values
Check input data files
Parse data files
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/lib/python3.13/site-packages/pycoQC/common.py:349: DtypeWarning: Columns (0: barcode_score, 1: barcode_front_score, 2: barcode_front_foundseq_length, 3: barcode_front_begin_index, 4: barcode_rear_score, 5: barcode_rear_foundseq_length, 6: barcode_rear_end_index) have mixed types. Specify dtype option on import or set low_memory=False.
  df =  pd.read_csv(fn_list[0], sep ="\t")
Merge data
Cleaning data
	Discarding lines containing NA values
		0 reads discarded
	Filtering out zero length reads
		360 reads discarded
	Sorting run IDs by decreasing throughput
		Run-id order ['5a9ea63e-e4a2-4dfe-914d-ed07de638538']
	Reordering runids
		Processing reads with Run_ID 5a9ea63e-e4a2-4dfe-914d-ed07de638538 / time offset: 0
	Cleaning up low frequency barcodes
		56 reads with low frequency barcode unset
	Cast value to appropriate type
	Reindexing dataframe by read_ids
		6,325,257 Final valid reads
Loading plotting interface
Generating HTML report
	Parsing html config file
	Running method summary
		Computing plot
Traceback (most recent call last):
  File "/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/bin/pycoQC", line 12, in <module>
    sys.exit(main_pycoQC())
             ~~~~~~~~~~~^^
  File "/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/lib/python3.13/site-packages/pycoQC/__main__.py", line 109, in main_pycoQC
    pycoQC (
    ~~~~~~~^
        summary_file = args.summary_file,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    ...<12 lines>...
        verbose = args.verbose,
        ^^^^^^^^^^^^^^^^^^^^^^^
        quiet = args.quiet)
        ^^^^^^^^^^^^^^^^^^^
  File "/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/lib/python3.13/site-packages/pycoQC/pycoQC.py", line 148, in pycoQC
    reporter.html_report(
    ~~~~~~~~~~~~~~~~~~~~^
        outfile=html_outfile,
        ^^^^^^^^^^^^^^^^^^^^^
        config_file=config_file,
        ^^^^^^^^^^^^^^^^^^^^^^^^
        template_file=template_file,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        report_title=report_title)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/lib/python3.13/site-packages/pycoQC/pycoQC_report.py", line 84, in html_report
    fig = method(**method_args)
  File "/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/lib/python3.13/site-packages/pycoQC/pycoQC_plot.py", line 188, in summary
    lab1, dd1 = self.__summary_data (df_level="all", groupby=groupby)
                ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/lib/python3.13/site-packages/pycoQC/pycoQC_plot.py", line 257, in __summary_data
    cells.append (self.__df_to_cell(df))
                  ~~~~~~~~~~~~~~~~~^^^^
  File "/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/lib/python3.13/site-packages/pycoQC/pycoQC_plot.py", line 277, in __df_to_cell
    l.append ("{:,.2f}".format(self._compute_N50(df["read_len"])))
                               ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
  File "/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/lib/python3.13/site-packages/pycoQC/pycoQC_plot.py", line 1467, in _compute_N50
    data.sort()
    ~~~~~~~~~^^
ValueError: sort array is read-only
=== nanoplot log tail ===
/fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_/bin/NanoPlot
WARNING:root:Plotly could not fetch or find Chrome automatically. Static exports may fail unless BROWSER_PATH is set. Details: 
This command requires Kaleido v1.0.0 or greater.
Install it using `pip install 'kaleido>=1.0.0'` or `pip install 'plotly[kaleido]'`."

=== conda env package versions ===
pycoQC=2.5.0.3
numpy=2.4.6
pandas=3.0.3
bokeh=<missing> No package metadata was found for bokeh
pycoQC v2.5.0.3
