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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PycoQC issue: Empty graph produced #149

Open dlbowie0 opened 6 months ago

dlbowie0 commented 6 months ago

command line used : pycoQC -f seq_summary.txt -a goi.bam -o output_pycoqc.html

After executing this ommand line in the pipeline, two of all the graphs produced by pycoQC are empty: image image

When I checked the .command.err file, the following error was stated: image

Numpy version installed == 1.26.4

Below you can find where in the pycoQC pcode `np.int' is stated: https://github.com/a-slide/pycoQC/blob/183711e794748c1f8b83ac96ce9e6fa402625bb8/pycoQC/pycoQC_plot.py#L1427 z = np.ones((len(bins), n_channels), dtype=np.int)