ddhb / workflow_of_chipseq Goto Github PK

Hi,

I am trying to replicate your code for my test samples but it resulted in error. Did you happen to see this before?

fitHM <- mosaicsFit( binHM, analysisType="IO", bgEst="rMOM" )
Info: background estimation based on robust method of moment.
Info: two-sample analysis (Input only).
Info: use adaptive griding.
Info: fitting background model...
Error in rlm.default(x, y, weights, method = method, wt.method = wt.method, :
'x' is singular: singular fits are not implemented in 'rlm'

Thanks,

Diya

hey，
when I used the example code to run the flow, first, the code genomeFile <- "BSgenome.Hsapiens.UCSC.hg19" ,how get it?
The above reference genome BSgenome. Hsapiens. UCSC. Hg19.fa . Is it need manual download to my work path?At the beginning, there was no download, the operation error, I can run after manual download. But the following second error occurs when comparing.I again, error : Failed to install the index package 'BSgenome.Hsapiens.UCSC.hg19.Rbowtie'. How can I solved it, thank you！

Matrix_file_control <- matrix(c("FileName",trimmed_control,"SampleName","Sample1"),nrow=2,ncol=2)
write.table(Matrix_file_control, file="sample_control.txt", sep="\t",row.names=FALSE, col.names=FALSE)
Matrix_file_case <- matrix(c("FileName",trimmed_case,"SampleName","Sample1"),nrow=2,ncol=2)
write.table(Matrix_file_case, file="sample_Case.txt", sep="\t",row.names=FALSE, col.names=FALSE)

Step 4-3. Assigning core and aligning to hg19 reference genome

no_cores <- detectCores()-1
cl <- makeCluster(no_cores)
Aligned_control<-qAlign(sampleFile=controlFile, genome=genomeFile,

•                     clObj=cl, alignmentsDir = working_dir)
  

alignment files missing - need to:
create alignment index for the genome
create 1 genomic alignment(s)
will start in ..9s..8s..7s..6s..5s..4s..3s..2s..1s
将程序包安装入'C:/Users/yangskyfucker/Documents/R/win-library/4.1'
(因为'lib'没有被指定)

• installing source package 'BSgenome.Hsapiens.UCSC.hg19.Rbowtie' ...
  ** using staged installation
  ** inst
  Warning in file.append(to[okay], from[okay]) : 文件追加时书写出错
  Warning in file.append(to[okay], from[okay]) : 文件追加时书写出错
  ** help
  *** installing help indices
  Warning in FUN(X[[i]], ...) : internal error -3 in R_decompress1
  Warning in close.connection(outcon) :
  Problem closing connection: No space left on device
  converting help for package 'BSgenome.Hsapiens.UCSC.hg19.Rbowtie'
  finding HTML links ... done
  Warning in FUN(X[[i]], ...) : internal error -3 in R_decompress1
  package html
  Rd warning: Problem closing connection: No space left on device
  ** building package indices
  Warning in FUN(X[[i]], ...) : internal error -3 in R_decompress1
  ** testing if installed package can be loaded from temporary location
  *** arch - i386
  Warning: 程辑包'GenomicRanges'是用R版本4.1.2 来建造的
  *** arch - x64
  Warning: 程辑包'GenomicRanges'是用R版本4.1.2 来建造的
  ** testing if installed package can be loaded from final location
  *** arch - i386
  Warning: 程辑包'GenomicRanges'是用R版本4.1.2 来建造的
  Warning in base::file("C:\Users\YANGSK1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2", :
  无法打开文件'C:\Users\YANGSK1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2': No space left on device
  Error in base::file("C:\Users\YANGSK1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2", :
  无法打开链结
  停止执行
  *** arch - x64
  Warning: 程辑包'GenomicRanges'是用R版本4.1.2 来建造的
  Warning in base::file("C:\Users\YANGSK1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2", :
  无法打开文件'C:\Users\YANGSK1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2': No space left on device
  Error in base::file("C:\Users\YANGSK1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2", :
  无法打开链结
  停止执行
  ERROR: loading failed for 'i386', 'x64'
• removing 'C:/Users/yangskyfucker/Documents/R/win-library/4.1/BSgenome.Hsapiens.UCSC.hg19.Rbowtie'
  Error in buildIndexPackage(proj@genome, proj@aligner, proj@alnModeID, :
  Failed to install the index package 'BSgenome.Hsapiens.UCSC.hg19.Rbowtie'
  In addition: Warning messages:
  1: In object@elementType :
  closing unused connection 5 (<-apps.corel.com:11244)
  2: In object@elementType :
  closing unused connection 4 (<-apps.corel.com:11244)
  3: In object@elementType :
  closing unused connection 3 (<-apps.corel.com:11244)
  4: In utils::install.packages(file.path(cacheDir, indexPackageName), :
  installation of package 'C:/Users/YANGSK~1/AppData/Local/Temp/RtmpMxfTDu/BSgenome.Hsapiens.UCSC.hg19.Rbowtie' had non-zero exit status