DRAGEN wgs_coverage_metrics RuntimeWarning encountering an invalid value

[jamigo]

Description of bug

Strangely, this error not always happens, not even with the same files individually but with a combination of them. I'm working with numpy v1.26.4 and plotly v5.19.0, and the set of wgs_coverage_metrics.csv files I'm attaching breaks numpy/core/_methods.py and therefore multiqc/plots/plotly/violin.py coming across an invalid value.

File that triggers the error

wgs_coverage_metrics.zip

MultiQC Error log

$ multiqc *

  /// MultiQC 🔍 | v1.20

|           multiqc | Search path : /path/to/csv/100.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/101.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/102.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/103.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/104.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/105.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/106.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/107.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/108.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/109.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/10.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/110.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/111.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/112.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/113.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/114.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/115.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/116.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/117.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/118.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/119.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/11.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/120.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/12.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/13.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/14.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/15.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/16.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/17.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/18.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/19.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/1.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/20.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/21.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/22.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/23.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/24.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/25.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/26.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/27.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/28.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/29.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/2.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/30.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/31.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/32.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/33.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/34.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/35.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/36.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/37.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/38.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/39.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/3.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/40.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/41.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/42.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/43.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/44.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/45.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/46.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/47.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/48.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/49.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/4.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/50.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/51.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/52.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/53.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/54.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/55.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/56.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/57.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/58.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/59.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/5.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/60.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/61.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/62.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/63.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/64.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/65.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/66.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/67.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/68.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/69.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/6.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/70.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/71.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/72.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/73.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/74.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/75.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/76.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/77.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/78.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/79.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/7.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/80.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/81.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/82.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/83.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/84.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/85.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/86.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/87.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/88.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/89.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/8.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/90.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/91.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/92.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/93.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/94.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/95.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/96.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/97.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/98.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/99.wgs_coverage_metrics.csv
|           multiqc | Search path : /path/to/csv/9.wgs_coverage_metrics.csv
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 120/120
/path/to/home/.local/lib/python3.9/site-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract
  x = asanyarray(arr - arrmean)
/path/to/home/.local/lib/python3.9/site-packages/multiqc/plots/plotly/violin.py:548: RuntimeWarning: invalid value encountered in s                                                                                                                                              ubtract
  z_scores = np.abs((values - mean) / std_dev)
|            dragen | Found 120 reports
|           multiqc | Report      : multiqc_report.html
|           multiqc | Data        : multiqc_data
|           multiqc | MultiQC complete

Before submitting

• I have read the troubleshooting documentation.
• I am using the latest release of MultiQC.
• I have included a full MultiQC log, not truncated.
• I have attached an input file (.zip if necessary) that triggers the error.

[vladsavelyev]

Thanks @jamigo for testing and reporting issues.

This is just a warning from the violin plot outlier detection algorithm. It still generates a correct report.

It is caused by DRAGEN reporting Inf values for Median autosomal coverage ratio over genome in wgs_coverage_metrics.csv, e.g.:

COVERAGE SUMMARY,,Mean/Median autosomal coverage ratio over genome,inf

Those Infs are then passed to the violin plot's outlier detection algorithm, which triggers this warning as numpy doesn't handle Inf values.

I now added a check to ignore Inf in the violin plots, as they don't make much sense there.

Thank you again!