Q: Many empty plots

[sklages]

I installed pycoQC without any issues using conda. I ran it on a standard MinION run (FLO-MIN106/SQK-ULK001, basecalled with guppy 6.0.1), again, without any issues.

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 ['60e1f540c15569d8c138033a157ac5633a5ba63e']
    Reordering runids
        Processing reads with Run_ID 60e1f540c15569d8c138033a157ac5633a5ba63e / time offset: 0
    Cast value to appropriate type
    Reindexing dataframe by read_ids
        54,160 Final valid reads
Loading plotting interface
Generating HTML report
    Parsing html config file
    Running method summary
        Computing plot
    Running method barcode_summary
        No barcode information available
    Running method run_id_summary
        There is only one run_id
    Running method read_len_1D
        Computing plot
    Running method align_len_1D
        No Alignment information available
    Running method read_qual_1D
        Computing plot
    Running method align_score_1D
        No align score information available
    Running method read_len_read_qual_2D
        Computing plot
    Running method read_len_align_len_2D
        No Alignment information available
    Running method align_len_align_score_2D
        No align score information available
    Running method read_qual_align_score_2D
        No align score information available
    Running method output_over_time
        Computing plot
    Running method len_over_time
        Computing plot
    Running method qual_over_time
        Computing plot
    Running method barcode_counts
        No barcode information available
    Running method channels_activity
        Computing plot
    Running method alignment_summary
        No Alignment information available
    Running method alignment_rate
        No align score information available
    Running method alignment_coverage
        No Alignment information available
    Loading HTML template
    Rendering plots in d3js
    Writing to HTML file

Quite a few plots are empty (no plotting):

• "Basecalled reads length"
• "Reads PHRED quality"
• "Read length over time"
• "Mean read quality over time".

And I have no idea why. The solution is probably simple .. but currently I have no clue.

Screenshots just one example

• OS: Linux, custom (server side), Python 3.9.5
• Browser (Vivaldi, FF, Safari, all on MacOS Monterey 12.2.1) on Notebook

I am sure I missed something .. any idea?

[sklages]

no response, no activity in project.

[sanchari24]

Hi did you solve this problem ?

[sklages]

I didn't. I just do not use pycoQC ..