PlotDenoisedCopyRatios Error

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Indrani Datta

• March 12, 2024 15:50

REQUIRED for all errors and issues:
GATK 4.3.0.0 

gatk PlotDenoisedCopyRatios \
    --standardized-copy-ratios /home/jupyter/notebooks/3-somatic-cna/sandbox/tumor.standardizedCR.tsv \
    --denoised-copy-ratios /home/jupyter/notebooks/3-somatic-cna/sandbox/tumor.denoisedCR.tsv \
    --sequence-dictionary /home/jupyter/notebooks/3-somatic-cna/ref/Homo_sapiens_assembly38.dict \
    --minimum-contig-length 46709983 \
    --output-prefix T19_clean \
    -O /home/jupyter/notebooks/3-somatic-cna/sandbox/cna_plots

Error:

Stderr: Usage: %prog [options]

NA: error: Error in getopt(spec = spec, opt = args) : long flag "args" is invalid

 

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  Gökalp Çelik

  • March 12, 2024 15:57

  Hi Indrani Datta

  This error is related to the R version that is in effect with your environment. PlotDenoisedCopyRatios is expecting an older version of R and r-optparse package however new versions of the r-optparse package does not use the args flag. 

  The required versions are listed below. 

  r-base                    3.6.2
  r-optparse                1.6.4

  I hope this helps. 

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  Indrani Datta

  • March 12, 2024 16:02

  Thank you.

  Indrani

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  Tushar Sharma

  • November 27, 2025 19:58

  Hi Indrani,

  I'm getting the same issue. Can you confirm if the suggested fix worked for you?

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