Question

我正在使用命令Rscript在unix服务器上运行R脚本。该程序计算重新编码的基因型之间的不同Ts和Tv。脚本似乎工作正常，直到它在未知时间内随机暂停（CPU到0.0％）。它有时后来又重新开始，但我在暂停时找不到任何模式。

它仅在以下for循环中停止：

#difference between different id
diffs <- NULL
for (i in 1:1091){
  # Start the clock
  ptm <- proc.time()
  print(i) 
  print(ptm)
  diffs <- NULL
  diffs <- abs(mdata[,4:ncol(mdata)]-cbind(mdata[,(4+i):ncol(mdata)],mdata[,4:(3+i)]))
  diffs <- cbind(diffs,pos_cpg)
  TCcount[i,] <- colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% TC),ncol=1092)) + 2*colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% TC2),ncol=1092))
  print('TC gelukt')
  TAcount[i,] <- colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% TA),ncol=1092)) + 2*colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% TA2),ncol=1092))
  print('TA gelukt')
  TGcount[i,] <- colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% TG),ncol=1092)) + 2*colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% TG2),ncol=1092))
  print('TG gelukt')
  CGcount[i,] <- colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% CG),ncol=1092)) + 2*colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% CG2),ncol=1092))
  print('CG gelukt')
  CAcount[i,] <- colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% CA),ncol=1092)) + 2*colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% CA2),ncol=1092))
  print('CA gelukt')
  GAcount[i,] <- colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% GA),ncol=1092)) + 2*colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% GA2),ncol=1092))
  print('GA gelukt')
  GAcpg[i,] <- colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% GA),ncol=1092)==(diffs[,ncol(diffs)])-((matrix((diffs[,1:(ncol(diffs)-1)] %in% GA),ncol=1092)==(diffs[,ncol(diffs)]))-(matrix((diffs[,1:(ncol(diffs)-1)] %in% GA),ncol=1092)))) + 2*colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% GA2),ncol=1092)==(diffs[,ncol(diffs)])-((matrix((diffs[,1:(ncol(diffs)-1)] %in% GA2),ncol=1092)==(diffs[,ncol(diffs)])-matrix((diffs[,1:(ncol(diffs)-1)] %in% GA2),ncol=1092))))
  print('GAcpg gelukt')
  TCcpg[i,] <- colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% TC),ncol=1092)==(diffs[,ncol(diffs)])-((matrix((diffs[,1:(ncol(diffs)-1)] %in% TC),ncol=1092)==(diffs[,ncol(diffs)])-matrix((diffs[,1:(ncol(diffs)-1)] %in% TC),ncol=1092)))) + 2*colSums(matrix((diffs[,1:(ncol(diffs)-1)] %in% TC2),ncol=1092)==(diffs[,ncol(diffs)])-((matrix((diffs[,1:(ncol(diffs)-1)] %in% TC2),ncol=1092)==(diffs[,ncol(diffs)])-matrix((diffs[,1:(ncol(diffs)-1)] %in% TC2),ncol=1092))))
  print('TCcpg gelukt')
  ratio1 <- mean(CAcount[i,]/TAcount[i,])
  ratio2 <- mean(TGcount[i,]/CGcount[i,])
  print(ratio1)
  print(ratio2)
  rm(diffs)
  Ts[i,] <- TCcount[i,] + GAcount[i,]
  print('Ts gelukt')
  Tv[i,] <- TAcount[i,] + TGcount[i,] + CAcount[i,] + CGcount[i,]
  print('Tv gelukt')
  TsCpG[i,] <- TCcpg[i,] + GAcpg[i,]
  print('TsCpG gelukt')
  CTnCpG[i,] <- TCcount[i,] - TCcpg[i,]
  print('CTnCpG gelukt')
  GAnCpG[i,] <- GAcount[i,] - GAcpg[i,]
  print('GAnCpG gelukt')
  # Stop the clock
  print(proc.time())
  tijd <- proc.time() - ptm
  print(paste(i,'gedaan','in',tijd[3],sep=' '))
  save(TC,file='TC.Rda')
  save(TA,file='TA.Rda')
  save(TG,file='TG.Rda')
  save(CA,file='CA.Rda')
  save(CG,file='CG.Rda')
  save(GA,file='GA.Rda')
  save(CTnCpG,file='CTnCpG.Rda')
  save(GAnCpG,file='GAnCpG.Rda')
  save(Ts,file='Ts.Rda')
  save(Tv,file='Tv.Rda')
  save(TsCpG,file='TsCpG.Rda')
  print('alles opgeslaan')
}

print语句是控制输出，用于确定暂停发生的位置。矩阵mdata在第4列到第二列的第二列中都有数字重新编码的基因型，最后一列包含一个0或1的值，告诉该位置是否为已知的CpG位置。

有人看到这个脚本会随机暂停的原因吗？

R-script在Unix服务器上意外挂起

0 个答案: