purple fails with R error in nf-core/oncoanalyser

[bounlu]

I was testing pipeline_v6.0 branch of nf-core/oncoanalyser in targeted mode. purple failed as below only for some of the samples. Same issue as before. Wondering what could be wrong with these samples?

ERROR ~ Error executing process > 'NFCORE_ONCOANALYSER:TARGETED:PURPLE_CALLING:PURPLE (220034479)'

Caused by:
  Process `NFCORE_ONCOANALYSER:TARGETED:PURPLE_CALLING:PURPLE (220034479)` terminated with an error exit status (1)


Command executed:

  purple \
      -Xmx12240656794 \
       \
      -tumor 220034479 \
       \
      -amber amber \
      -cobalt cobalt \
      -somatic_sv_vcf 220034479.esvee.somatic.vcf.gz \
       \
      -somatic_vcf 220034479.sage.somatic.pave.vcf.gz \
       \
      -ref_genome GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
      -ref_genome_version 38 \
      -driver_gene_panel DriverGenePanel.tso500.38.tsv \
      -ensembl_data_dir ensembl_data \
      -somatic_hotspots KnownHotspots.somatic.38.vcf.gz \
      -germline_hotspots KnownHotspots.germline.38.vcf.gz \
      -target_regions_bed target_regions_definition.tso500.38.bed.gz \
      -target_regions_ratios target_regions_ratios.tso500.38.tsv \
      -target_regions_msi_indels target_regions_msi_indels.tso500.38.tsv \
      -germline_del_freq_file cohort_germline_del_freq.38.csv \
      -gc_profile GC_profile.1000bp.38.cnp \
      -circos $(which circos) \
      -threads 2 \
      -output_dir purple/
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_ONCOANALYSER:TARGETED:PURPLE_CALLING:PURPLE":
      purple: $(purple -version | sed 's/^.* //')
  END_VERSIONS

Command exit status:
  1

Command output:
  09:09:01.788 [INFO ] Purple version 4.1
  09:09:01.796 [INFO ] output directory: purple/
  09:09:01.808 [INFO ] reference(NONE) tumor(220034479) running on target-regions only
  09:09:01.995 [INFO ] using ref genome: V38
  09:09:07.919 [INFO ] loaded 0 germline deletions frequencies from file: cohort_germline_del_freq.38.csv
  09:09:07.926 [INFO ] loaded 130 MSI indels from file(target_regions_msi_indels.tso500.38.tsv)
  09:09:07.926 [INFO ] target regions: tml(1.0) tmb(0.05) msiIndels(220.0) msiAF(2-3 base=0.15 4 base=0.08) codingBaseFactor(150000)
  09:09:08.420 [INFO ] loaded 7282 target regions bases(total=1314771 coding=1309730) from file(target_regions_definition.tso500.38.bed.gz)
  09:09:08.422 [INFO ] reading GC Profiles from GC_profile.1000bp.38.cnp
  09:09:14.001 [INFO ] reading Amber QC from amber/220034479.amber.qc
  09:09:14.028 [INFO ] reading Amber BAFs from amber/220034479.amber.baf.tsv.gz
  09:09:14.055 [INFO ] reading Amber PCFs from amber/220034479.amber.baf.pcf
  09:09:14.360 [INFO ] Amber average tumor depth(2064) ambiguous BAF(0.510)
  09:09:14.361 [INFO ] reading Cobalt tumor segments from cobalt/220034479.cobalt.ratio.pcf
  09:09:14.392 [INFO ] reading Cobalt ratios from cobalt/220034479.cobalt.ratio.tsv.gz
  09:09:23.398 [INFO ] loaded 191 somatic SVs from 220034479.esvee.somatic.vcf.gz
  09:09:25.556 [INFO ] loaded 14747 somatic variants from 220034479.sage.somatic.pave.vcf.gz
  09:09:25.557 [INFO ] sample gender is female
  09:09:25.557 [INFO ] purple output directory: purple/
  09:09:25.588 [INFO ] applying segmentation
  09:09:25.588 [INFO ] merging reference and tumor ratio break points
  09:09:29.829 [INFO ] fitting purity
  09:09:32.984 [INFO ] enriching somatic variants
  09:09:33.400 [INFO ] load(3.0 tml=121.7045) msiIndels(0 perMb=0.0000) burden(5.0 perMb=6.0852)
  09:09:34.725 [INFO ] generating QC Stats
  09:09:34.822 [INFO ] generating charts
  09:09:34.907 [INFO ] generating 220034479.circos.png via command: /usr/local/bin/circos -nosvg -conf purple/circos/220034479.circos.conf -outputdir purple/plot -outputfile 220034479.circos.png
  09:09:34.907 [INFO ] generating 220034479.input.png via command: /usr/local/bin/circos -nosvg -conf purple/circos/220034479.input.conf -outputdir purple/plot -outputfile 220034479.input.png
  09:09:56.444 [FATAL] error executing R script
  09:09:56.447 [WARN ] error generating charts
  09:09:56.448 [ERROR] charting error: java.lang.Exception: charting failed

Command error:
  Fontconfig error: No writable cache directories
  Error in `scale_y_continuous()`:
  ! Discrete values supplied to continuous scale.
  i Example values: NA, NA, NA, NA, and NA
  Backtrace:
       x
    1. \-global clonality_plot(somaticBuckets, clonalityModel)
    2.   \-cowplot::plot_grid(...)
    3.     \-cowplot::align_plots(...)
    4.       \-base::lapply(...)
    5.         \-cowplot (local) FUN(X[[i]], ...)
    6.           +-cowplot::as_gtable(x)
    7.           \-cowplot:::as_gtable.default(x)
    8.             +-cowplot::as_grob(plot)
    9.             \-cowplot:::as_grob.ggplot(plot)
   10.               \-ggplot2::ggplotGrob(plot)
   11.                 +-ggplot2::ggplot_gtable(ggplot_build(x))
   12.                 | \-ggplot2:::attach_plot_env(data$plot$plot_env)
   13.                 |   \-base::options(ggplot2_plot_env = env)
   14.                 +-ggplot2::ggplot_build(x)
   15.                 \-ggplot2:::ggplot_build.ggplot(x)
   16.                   \-layout$train_position(data, scale_x(), scale_y())
   17.                     \-ggplot2 (local) train_position(..., self = self)
   18.                       \-self$facet$train_scales(...)
   19.                         \-ggplot2 (local) train_scales(...)
   20.                           \-ggplot2:::scale_apply(layer_data, y_vars, "train", SCALE_Y, y_scales)
   21.                             \-base::lapply(...)
   22.                               \-ggplot2 (local) FUN(X[[i]], ...)
   23.                                 \-base::lapply(...)
   24.                                   \-ggplot2 (local) FUN(X[[i]], ...)
   25.                                     \-scales[[i]][[method]](data[[var]][scale_index[[i]]])
   26.                                       \-ggplot2 (local) train(..., self = self)
   27.                                         \-cli::cli_abort(...)
   28.                                           \-rlang::abort(...)
  Warning messages:
  1: Removed 201 rows containing non-finite outside the scale range
  (`stat_align()`). 
  2: Removed 1 row containing missing values or values outside the scale range
  (`geom_bar()`). 
  3: Removed 201 rows containing missing values or values outside the scale range
  (`geom_line()`). 
  4: Removed 331 rows containing missing values or values outside the scale range
  (`geom_line()`). 
  Execution halted
  sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
  java.lang.Exception: charting failed
  	at com.hartwig.hmftools.purple.plot.Charts.write(Charts.java:61)
  	at com.hartwig.hmftools.purple.PurpleApplication.performFit(PurpleApplication.java:322)
  	at com.hartwig.hmftools.purple.PurpleApplication.run(PurpleApplication.java:128)
  	at com.hartwig.hmftools.purple.PurpleApplication.main(PurpleApplication.java:465)

Work dir:
  /data/nextflow/oncoanalyser/work/81/c2c7x8bc5afcd3786df0a23d0c42c3

Container:
  quay.io/biocontainers/hmftools-purple:4.1_beta--hdfd78af_2

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details

[bounlu]

It turns out that the error is coming from these lines where $sample.purple.somatic.clonality.tsv file is not filtered properly as it contains bucketWeight column with NaN values but isValid column is still TRUE. This causes error later in the clonality_plot with NA values.