我正在运行一些质量控制，使用我的MacBook Air OS X El Capitan上最新的MEDIPS软件包，内存为4GB。我能够运行其他质量控制：饱和分析和序列模式覆盖很好。但是这是我在运行CpG浓缩检查后收到的错误。我运行它的文件大约是3GB，我只选择了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)
我还没有在网上找到一个可靠的答案，但这是R告诉我内存不足或Biostrings出错的方法吗？我在运行此代码之前已更新Biostings。
让我知道你的想法。我对R编程很新，所以简化会很受欢迎。
答案 0 :(得分：0)
我遇到的是，当Biostrings版本为2.48.0时会发生该错误，而当版本为2.50.2时该错误会消失。