plotting error with cell line samples and --min-purity 0.98 --max-purity 0.99

[ThomasGro]

with the following settings I get a plotting error for all my ~400 cell line samples and Mutect2 VCF:

--genome GRCh38
--min-af 0.03
--min-purity 0.98
--max-purity 0.99
--min-ploidy 1.4
--max-ploidy 6.0
--max-copy-number 7
--max-segments 300
--max-non-clonal 0.2
--min-total-counts 100
--model-homozygous 
--model beta
--fun-segmentation CBS
--post-optimize 
--seed 42 

example SDTOUT,SDTERR: ... Generating output files... Warning message: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will be forced to unique rownames Error in plot.window(...) : need finite 'ylim' values Calls: plotAbs ... .plotTypeBAF -> plot -> plot.default -> localWindow -> plot.window In addition: Warning messages: 1: In .Call(.make_vcf_geno, filename, fixed, names(geno), as.list(geno), : converting NULL pointer to R NULL 2: In plot.default(xLogRatio, logRatio$log.ratio, ylab = "Copy Number log-ratio", : NaNs produced Execution halted

PureCN did not finish successfully for sample CELL_143B!

Any idea what the problem could be or how I can track the problem?

[lima1]

Hmm, can't remember seeing this one before. Not sure it's related, but do you run into (other) issues with --genome hg38? PureCN pulls some genome specific annotation files from Bioconductor, and not sure GRC38 works here. I'm might have addressed it, but can't remember.

If not, can you share the full log file of this sample?

[lima1]

Actually, before you change anything, can you make sure that you use the latest stable version? I vaguely remember fixing a crash similar to that.

[ThomasGro]

Unfortunately this version is part of a workflow systen and cannot easily and quickly be updated. But I have received a hint in the same direction from a colleague: a newer version of PureCN fixed the issue. Thank you for following up. From: Markus Riester @.> Sent: Samstag, 20. Januar 2024 00:51 To: lima1/PureCN @.> Cc: Thomas Grombacher @.>; Author @.> Subject: Re: [lima1/PureCN] plotting error with cell line samples and --min-purity 0.98 --max-purity 0.99 (Issue #344)

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Actually, before you change anything, can you make sure that you use the latest stable version? I vaguely remember fixing a crash similar to that.

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[lima1]

Looks like this is the previous bug: https://github.com/lima1/PureCN/issues/260

Maybe try reducing the max-ploidy to something lower if you can't update now. 6 should be super rare.