Hi Everyone, I encountered this error with using this script: Error:

Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS (A4_H_H3K27Ac)'

Caused by:
  Process `NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS (A4_H_H3K27Ac)` terminated with an error exit status (1)

Command executed:

  RUN_SPP=`which run_spp.R`
  Rscript  -e "library(caTools); source(\"$RUN_SPP\")" -c="A4_H_H3K27Ac.mLb.clN.sorted.bam" -savp="A4_H_H3K27Ac.spp.pdf" -savd="A4_H_H3K27Ac.spp.Rdata" -out="A4_H_H3K27Ac.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: A4_H_H3K27Ac.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: A4_H_H3K27Ac.spp.Rdata 
  plot pdf filename: A4_H_H3K27Ac.spp.pdf 
  result filename: A4_H_H3K27Ac.spp.out 
  Overwrite files?: FALSE
  
  Reading ChIP tagAlign/BAM file A4_H_H3K27Ac.mLb.clN.sorted.bam 
  opened /tmp/RtmpwcvaIx/A4_H_H3K27Ac.mLb.clN.sorted.tagAlign29344786f7
  done. read 55416748 fragments
  ChIP data read length 150 
  Calculating peak characteristics
  Minimum cross-correlation value 0.3306441 
  Minimum cross-correlation shift 1500 
  Top 3 cross-correlation values NA 
  Top 3 estimates for fragment length NA 
  Window half size NA 
  Phantom peak location 140 
  Phantom peak Correlation 0.6661341 
  Normalized Strand cross-correlation coefficient (NSC) NA 
  Relative Strand cross-correlation Coefficient (RSC) NA 

Command error:
  WARNING: Skipping mount /cluster/software/modules-sw/singularity/ce-3.9.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  Loading required package: Rcpp
  ################
  ChIP data: A4_H_H3K27Ac.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: A4_H_H3K27Ac.spp.Rdata 
  plot pdf filename: A4_H_H3K27Ac.spp.pdf 
  result filename: A4_H_H3K27Ac.spp.out 
  Overwrite files?: FALSE
  
  Reading ChIP tagAlign/BAM file A4_H_H3K27Ac.mLb.clN.sorted.bam 
  opened /tmp/RtmpwcvaIx/A4_H_H3K27Ac.mLb.clN.sorted.tagAlign29344786f7
  done. read 55416748 fragments
  ChIP data read length 150 
  Calculating peak characteristics
  Minimum cross-correlation value 0.3306441 
  Minimum cross-correlation shift 1500 
  Top 3 cross-correlation values NA 
  Top 3 estimates for fragment length NA 
  Window half size NA 
  Phantom peak location 140 
  Phantom peak Correlation 0.6661341 
  Normalized Strand cross-correlation coefficient (NSC) NA 
  Relative Strand cross-correlation Coefficient (RSC) NA 
  Error in if ((crosscorr$rel.phantom.coeff >= 0) & (crosscorr$rel.phantom.coeff <  : 
    missing value where TRUE/FALSE needed
  Calls: source -> withVisible -> eval -> eval
  Execution halted

Work dir:
  /beevol/home/liutian/Documents/cut_and_run/Foreman/ChIP_Seq/fastq_files/work/fe/3cc1e598f71ada27f13077cd426583

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

My script: nextflow run nf-core/chipseq -profile singularity --input Foreman_lab_ChIPseq.csv --genome GRCh38 --narrow_peak false --read_length 150 --macs_gsize 2862089864 --outdir $OUTPUT --skip_spp -resume What should I do to fix this error? Thanks!

hi, see my answer