Filter out MACS results with zero peaks

[orzechoj]

I'm getting this error when I'm running ChIP-Seq Best Practice v1.0 with nextflow v 0.31.1, on Uppmax/ bianca.

ERROR ~ Error executing process > 'chippeakanno (ALBB13_137_H3K27me3_peaks)'

Caused by:
  Process `chippeakanno (ALBB13_137_H3K27me3_peaks)` terminated with an error exit status (1)

Command executed:

  post_peak_calling_processing.r /usr/local/lib/R/library /home/jacke/bin/chipseq/blacklists/hg19-blacklist.bed genes.gtf <a lot of data sets here..>

Command exit status:
  1

Command output:
  (empty)

Command error:
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from ‘package:stats’:
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from ‘package:base’:
  
      anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
      colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
      grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
      mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
      rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
      table, tapply, union, unique, unsplit, which, which.max, which.min
  
  Loading required package: S4Vectors
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:base’:
  
      expand.grid
  
  Loading required package: IRanges
Loading required package: GenomeInfoDb
  Loading required package: ChIPpeakAnno
  Loading required package: grid
  Loading required package: Biostrings
  Loading required package: XVector
  
  Attaching package: ‘Biostrings’
  
  The following object is masked from ‘package:base’:
  
      strsplit
  
  Loading required package: VennDiagram
  Loading required package: futile.logger
  
  Warning message:
  In read.dcf(con) :
    URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
  Loading required package: rtracklayer
  Loading required package: doParallel
  Loading required package: foreach
  Loading required package: iterators
  Error in S4Vectors:::normalize_names_replacement_value(value, x) : 
    attempt to set too many names (2) on IRanges object of length 0
  Calls: annotatePeakInBatch ... names<- -> names<- -> names<- -> names<- -> <Anonymous>
  Execution halted

I used the following command to run:

nohup nextflow run /home/jacke/bin/chipseq \
    --singleEnd \
     --reads '*.fastq.gz' \
     --genome GRCh37 \
     --project sens2017533 \
     --macsconfig 'macssetup.config' \
     -resume \
     -with-trace \
     -with-dag flowchart.pdf \
      --broad \
     --blacklist_filtering \
     -profile uppmax \
     -with-singularity /home/jacke/bin/singularity_images/nfcore-chipseq.img &

And most, but not all, MACS 2 jobs have finished ok.

EDIT: Two of the peak files from MACS contain no peaks. That is probably what gives the error.

[drpatelh]

Closed in favour of #35