ANNOTATE:CHIPSEEKER_PEAKPLOT failed due to memory allocation

[slsevilla]

Description of the bug

Job failed because there wasn't enough memory allocated. This is a little more problematic than just updating resources because for every job that failed, 20+ subjobs were created (this is running in parallel) which did not have enough memory. Since the max attempts is 2 this can really escalate quickly. We need to

• update the memory for this module
• decrease retries to 1x

Command output:
  GRanges object with 66127 ranges and 2 metadata columns:
            seqnames              ranges strand |    pvalue    qvalue
               <Rle>           <IRanges>  <Rle> | <numeric> <numeric>
        [1]     chr1       181444-181645      * |     15.18     14.75
        [2]     chr1       181913-182114      * |     10.54     10.18
        [3]     chr1       186155-186356      * |      5.85      5.59
        [4]     chr1       186835-187036      * |      3.20      3.03
        [5]     chr1       267916-268117      * |     64.14     63.30
        ...      ...                 ...    ... .       ...       ...
    [66123]     chrX 155651333-155651534      * |      3.81      3.62
    [66124]     chrX 155662420-155662621      * |      6.09      5.83
    [66125]     chrY   11085350-11085551      * |      2.64      2.50
    [66126]     chrY   11156173-11156374      * |     16.16     15.71
    [66127]     chrY   11156459-11156660      * |     12.06     11.67
    -------
    seqinfo: 24 sequences from an unspecified genome; no seqlengths
  >> binning method is used...2024-02-23 00:28:55
  >> preparing body regions by gene... 2024-02-23 00:28:55
  >> preparing tag matrix by binning...  2024-02-23 00:28:55 
  >> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2024-02-23 00:28:55
  >> 87 peaks(0.4930296%), having lengths smaller than 800bp, are filtered... 2024-02-23 00:29:15

Command error:
  Warning messages:
  1: In normalizePath("~") :
    path[1]="/home/sevillas2": No such file or directory
  2: package 'dplyr' was built under R version 4.3.2 
  Error in t.star[r, ] <- res[[r]] : 
    number of items to replace is not a multiple of replacement length
  Calls: plotPeakProf2 ... plotAvgProf.binning.internal -> getTagCount -> getTagCiMatrix -> boot
  In addition: Warning message:
  In parallel::mclapply(seq_len(RR), fn, mc.cores = ncpus) :
    scheduled cores 63, 68, 69, 71, 76, 80, 82, 95, 96, 100, 110, 119 did not deliver results, all values of the jobs will be affected
  Execution halted

Command used and terminal output

Ran within NF workflow, but this is the specific command ran

 chipseeker_peakplot.R \
      --peak CTCF.gem.sorted.merged.consensus.bed \
      --outfile-prefix CTCF.gem \
      --genome-txdb TxDb.Hsapiens.UCSC.hg38.knownGene \
      --genome-annot org.Hs.eg.db

[slsevilla]

duplicate of #169