Hello,
I'm trying to run DiffBind with some new ChIP-Seq samples and I've posted my output errors below. The main error I keep encountering is that it cannot process my read files. All of my files look to be okay when I manually inspect them and they're successfully calling the correct files. I've included my R code and my error.
library (DiffBind)
setwd("/scratch/Samantha.nixon/BambedEzh2Stat3/")
samples <- read.csv("samplesheet_ezh2.csv")
ezh2 <- dba(sampleSheet=samples) plot(ezh2)
ezh2 <- dba.count(ezh2) warnings() ezh2 = dba.contrast(ezh2, minMembers=3)
ezh2 <- dba.analyze(ezh2) plot(ezh2)
Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from ‘package:base’:
aperm, apply, rowsum
480Ezh2 wildtype 1 bed
480DEzh2 mutant 2 bed
855Ezh2 wildtype 1 bed
855DEzh2 mutant 2 bed
234Ezh2 wildtype 1 bed
234DEzh2 mutant 2 bed
Error: Error processing one or more read files. Check warnings().
In addition: Warning messages:
1: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) :
scheduled cores 1, 4, 5, 6, 9 did not deliver results, all values of the jobs will be affected
2:
3:
4:
5:
6:
Execution halted
