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  • MEDIPS by Lukas Chavez in R

    I'm running a few quality controls using the most up to date MEDIPS package on my MacBook Air OS X El Capitan with 4GB of memory. I'm able to run the other quality controls: saturation analysis and sequence pattern coverage nicely. However this is the error I receive after running a CpG enrichment check. The file I ran it on is around 3GB and I only selected chr1:

    er = MEDIPS.CpGenrich(file=file,BSgenome=BSgenome, chr.select = chr.select, extend = extend,uniq = uniq)
    Reading bam alignment HCB3_45Low_merged_unique.bam
    Selecting chr1
    Total number of imported short reads: 3214352
    Extending reads...
    Creating GRange Object...
    Keep at most one 1 read mapping to the same genomic location.
    Number of remaining reads: 3211326
    Loading chromosome lengths for BSgenome.Hsapiens.UCSC.hg19...
    Calculating CpG density for given regions...

    *** caught segfault ***
    address 0x7fff4c68f380, cause 'memory not mapped'

    Traceback:
    1: .Call(.NAME, ..., PACKAGE = PACKAGE)
    2: .Call2("new_CHARACTER_from_XStringSet", x, xs_dec_lkup(x), PACKAGE = "Biostrings")
    3: .local(x, ...)
    4: as.character(ans)
    5: as.character(ans)
    6: .local(x, ...)
    7: getSeq(dataset, names = space(x), start = start(x), end = end(x), as.character = TRUE)
    8: getSeq(dataset, names = space(x), start = start(x), end = end(x), as.character = TRUE)

    I haven't found a solid answer online, but is this R's way of telling me I ran out of memory or a bug with Biostrings? I've updated Biostings prior to running this.

    Let me know what you think. Im very new to R programming, so simplifying would be appreciated.

    Thanks!

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