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.

[Sanchari Sircar]

Hi did you solve this problem ?

[sklages]

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