Error in h(simpleError(msg, call))

[kristianunger]

Hi Markus,

I recently ran into the following error when running

It's the latest PureCN version 2.11.0 as part of the the docker image kristianunger/purecndocker:0624

singularity run -B purecndocker_0624.sif Rscript $PURECN/PureCN.R --out $OUT/$SAMPLEIDOUT --tumor {SAMPLEID}_coverage_loess.txt.gz --fun-segmentation PSCBS --sampleid $SAMPLEID --vcf $INPUT_VCF --statsfile $statsfile --normaldb $normal_db/normalDB_agilent_v6_hg38.rds --intervals $baits --snpblacklist $srr --genome hg38 --postoptimize --model betabin --force --seed 123

INFO [2024-06-02 14:48:31] Segmenting data... INFO [2024-06-02 14:48:32] Interval weights found, will use weighted PSCBS. Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'median': non-numeric argument to mathematical function Calls: runAbsoluteCN ... .log_level -> layout -> median -> .handleSimpleError -> h In addition: Warning message: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will be forced to unique rownames Execution halted

Can you give me an idea what might be the problem?

Best wishes

Kristian

[kristianunger]

Setting --min-base-quality 20 in PureCN.R solved the problem. Without setting, no variants remained on targets which seemed to have caused the error.