Signature quantification step fails when running pipeline on just one sample

[ahwanpandey]

Hi,

The step DINCALCILAB_SAMURAI:SAMURAI:SOLID_BIOPSY:CIN_SIGNATURE_QUANTIFICATION fails when I run the pipeline on just one sample. I believe it is the "plotSampleByComponent" function:

Starting Signature Extraction...
checkChromosomeFormat: dropping 'chr' prefix
Saving RDS dataset...
Error in stats::heatmap(x = plotData, scale = "col", Colv = NA, ...) :
  'x' must have at least 2 rows and 2 columns
Calls: plotSampleByComponent -> <Anonymous>
Execution halted

I have manged to fix this by changing the following line of code:

from:

png(filename="ascat_sc_plot_by_component.png")
plotSampleByComponent(object = cnobj)
dev.off()

to:

png(filename="ascat_sc_plot_by_component.png")
#plotSampleByComponent(object = cnobj)
plotActivities(object = cnobj, type = "threshold")
dev.off()

As you can see, I still need to create the file "ascat_sc_plot_by_component.png" for the pipeline to finish without errors, so I've jun run the plotActivities function again just to create this file.

Hope that makes sense and is an easy change at your end?

Thanks!
Ahwan

[lbeltrame]

Thanks @ahwanpandey . It seems that the code (upstream) won't work if you have only one sample, so we'll adjust it. We're in the middle of a big update for ichorCNA that uncovered a few upstream bugs - so we'll get to it once we're done, I'm fairly confident that being a trivial change I can easily have it in the next release.

[lbeltrame]

@ahwanpandey I did change that part, would you be able to test and see whether it's fixed for you?

[ahwanpandey]

@lbeltrame just ran with the update, and got this error I had seen before. Basically like I had mentioned in the original issue, the pipeline is still looking for this file "ascat_sc_plot_by_component.png" which I had "fixed" by creating that file just as a placeholder.

Dec-12 10:22:57.009 [TaskFinalizer-3] ERROR nextflow.processor.TaskProcessor - Error executing process > 'DINCALCILAB_SAMURAI:SAMURAI:SOLID_BIOPSY:CIN_SIGNATURE_QUANTIFICATION (Extracting Signatures)'

Caused by:
  Missing output file(s) `*_plot_by_component.png` expected by process `DINCALCILAB_SAMURAI:SAMURAI:SOLID_BIOPSY:CIN_SIGNATURE_QUANTIFICATION (Extracting Signatures)`


Command executed:

  compute_signatures.R \
      --seg_file 'all_segments_ascat_sc_signatures.seg' \
      --cpus '1' \
      --genome hg38 --projectname 'ascat_sc'

  cat <<-END_VERSIONS > versions.yml
  "DINCALCILAB_SAMURAI:SAMURAI:SOLID_BIOPSY:CIN_SIGNATURE_QUANTIFICATION":
      CINSignatureQuantification: 0.1
  END_VERSIONS

Command exit status:
  0

Command output:
  null device
            1
  null device
            1

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Starting Signature Extraction...
  checkChromosomeFormat: dropping 'chr' prefix
  Saving RDS dataset...
  Fontconfig error: No writable cache directories
  Complete.

Work dir:
  /researchers/ahwan.pandey/Projects/WholeGenome/Project_EC/AZ_ADC/analysis_31_10_2025/run1/Sample_66130_Ascites/work/fb/2cc78463fd6626527b818b4304fbc0

Container:
  /config/binaries/singularity/containers_devel/nextflow/quay.io-dincalcilab-cinsignaturequantification-1.1.2-af6117b.img

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

[lbeltrame]

Whoops! I thought I set it as optional, turns out I didn't... will fix.

[lbeltrame]

@ahwanpandey Feel free to test at your leisure and let me know if it works.

[ahwanpandey]

@lbeltrame the pipeline completed with no issues, thanks!