RIPSeeker ERROR message with Ripseek function

Question

[ximena.garate]

Hi everyone,

I'm analyzing some RIP-seq data using the RIPSeeker package of Bioconductor and I keep getting an error message and don't know what I should change to make it work...

This is how I set all parameters:

cNAME <- "Aligned.out_1B_sort" outDir <- file.path(getwd(), "RIPSeeker_analysis") binSize <- NULL minBinSize <- NULL maxBinSize <- NULL multicore <- TRUE strandType <- "+" biomart <- "ensembl" biomaRt_dataset <- "hsapiens_gene_ensembl" goAnno <- "org.Hs.eg.db"

seekOut.iPS_1 <- ripSeek(bamPath = "~/Desktop/AGO_IP/iPSrep1", cNAME = cNAME, reverseComplement = TRUE, genomeBuild = "hg38", strandType = strandType, uniqueHit = TRUE, assignMultihits = TRUE, rerunWithDisambiguatedMultihits = TRUE, binSize=binSize, minBinSize = minBinSize, maxBinSize = maxBinSize, biomart=biomart, goAnno = goAnno, biomaRt_dataset = biomaRt_dataset, multicore=multicore, outDir=outDir)

And the error message I got is: Error in mclapply(as.list(split(alignGR, seqnames(alignGR))), mainSeekSingleChrom, : 'mc.cores' must be >= 1

Does anyone know what this error means and how to fix it? Any suggestion will be much appreciated. Thanks Ximena

Answer 1

[Friederike]

posted in response to the same question in this post:

are you using a Windows machine? mclapply does not work on Windows. Apart from that, what happens when you set multicore <- FALSE?