PHANTOMPEAKQUALTOOLS throws stack overflow exception

[krokicki]

Description of the bug

PHANTOMPEAKQUALTOOLS throws a stack overflow exception on certain types of input data. This issue suggests a fix by increasing the default --max-ppsize. This is already implemented in MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS and should be added to PHANTOMPEAKQUALTOOLS as well.

Command used and terminal output

nextflow run main.nf -profile janelia --input samples.csv --read_length 50 --outdir ./results --fasta internal.fasta --gff internal.gff
ERROR ~ Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS (neg_rep1)'

Caused by:
  Process `NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS (neg_rep1)` terminated with an error exit status (1)

Command executed:

  RUN_SPP=`which run_spp.R`
  Rscript  -e "library(caTools); source(\"$RUN_SPP\")" -c="neg_rep1.mLb.clN.sorted.bam" -savp="neg_rep1.spp.pdf" -savd="neg_rep1.spp.Rdata" -out="neg_rep1.spp.out" -p=6

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS":
      phantompeakqualtools: 1.2.2
  END_VERSIONS

Command exit status:
  1

Command output:
  ################
  ChIP data: neg_rep1.mLb.clN.sorted.bam
  Control data: NA
  strandshift(min): -500
  strandshift(step): 5
  strandshift(max) 1500
  user-defined peak shift NA
  exclusion(min): 10
  exclusion(max): NaN
  num parallel nodes: 6
  FDR threshold: 0.01
  NumPeaks Threshold: NA
  Output Directory: .
  narrowPeak output file name: NA
  regionPeak output file name: NA
  Rdata filename: neg_rep1.spp.Rdata
  plot pdf filename: neg_rep1.spp.pdf
  result filename: neg_rep1.spp.out
  Overwrite files?: FALSE

  Reading ChIP tagAlign/BAM file neg_rep1.mLb.clN.sorted.bam
  opened /tmp/RtmpEulNd9/neg_rep1.mLb.clN.sorted.tagAlign2961e49a6f
  done. read 326050 fragments

Command error:
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  Loading required package: Rcpp
  Error: protect(): protection stack overflow
  Execution halted

Relevant files

No response

System information

No response

[krokicki]

Fixed by #371.