QQ Plot Error

[aaleksandrov95]

When running the pipeline, the generated report for some of the phenotypes does not always contain the QQ plot, instead showing:

QQ Plot
Error in if (is.unsorted(-ypvs)) ypvs = sort.int(ypvs, decreasing = TRUE): missing value where TRUE/FALSE needed
Error in methods::is(x, "qqPlotInfo"): object 'qqPrepare' not found

I looked into my results, and it seems to happen for phenotypes, where the p-values for some of the variants contain NaN values.

EDIT: I forgot to add the logs, my apologies.

./work/08$ cat 6337d26544fe60eefdc643c500cec7/.command.sh 
#!/bin/bash -ue
java -jar /opt/genomic-utils.jar csv-filter         --separator '       '         --output-sep '        '         --input BlutdrucksystolischmmHg.regenie.gz         --limit 2         --filter-column "LOG10P"         --gz         --output BlutdrucksystolischmmHg.regenie.tmp
csvtk sort BlutdrucksystolischmmHg.regenie.tmp -t -kLOG10P:nr | gzip >  BlutdrucksystolischmmHg.regenie.filtered.gz
rm BlutdrucksystolischmmHg.regenie.tmp

./work/08$ cat 6337d26544fe60eefdc643c500cec7/.command.log
Picked up JAVA_TOOL_OPTIONS: -Djdk.lang.Process.launchMechanism=vfork

genomic-utils 0.3.7
https://github.com/genepi/genomic-utils
(c) 2023 Lukas Forer and Sebastian Sch?nherr

Ignoring line 11189. Value 'NA' cannot be parsed.
Ignoring line 31339. Value 'NA' cannot be parsed.
Ignoring line 33364. Value 'NA' cannot be parsed.
Ignoring line 34436. Value 'NA' cannot be parsed.
Ignoring line 35160. Value 'NA' cannot be parsed.
Ignoring line 40564. Value 'NA' cannot be parsed.
Ignoring line 52187. Value 'NA' cannot be parsed.
Ignoring line 78387. Value 'NA' cannot be parsed.
Ignoring line 96562. Value 'NA' cannot be parsed.
Ignoring line 98599. Value 'NA' cannot be parsed.
Ignoring line 98964. Value 'NA' cannot be parsed.
Ignoring line 106249. Value 'NA' cannot be parsed.
Ignoring line 152650. Value 'NA' cannot be parsed.
Ignoring line 153719. Value 'NA' cannot be parsed.

[seppinho]

Thanks for letting us know. @johsr