> library(systemPipeR)

Loading required package: Rsamtools

Loading required package: GenomeInfoDb

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, colMeans,

    colnames, colSums, dirname, do.call, duplicated, eval, evalq,

    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,

    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,

    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,

    rowSums, sapply, setdiff, sort, table, tapply, union, unique,

    unsplit, which, which.max, which.min


Loading required package: S4Vectors

Loading required package: stats4


Attaching package: ‘S4Vectors’


The following object is masked from ‘package:base’:


    expand.grid


Loading required package: IRanges

Loading required package: GenomicRanges

Loading required package: Biostrings

Loading required package: XVector


Attaching package: ‘Biostrings’


The following object is masked from ‘package:base’:


    strsplit


Loading required package: ShortRead

Loading required package: BiocParallel

Loading required package: GenomicAlignments

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")'.



Attaching package: ‘Biobase’


The following object is masked from ‘package:BiocGenerics’:


    dims


Loading required package: DelayedArray

Loading required package: matrixStats


Attaching package: ‘matrixStats’


The following objects are masked from ‘package:Biobase’:


    anyMissing, rowMedians



Attaching package: ‘DelayedArray’


The following objects are masked from ‘package:matrixStats’:


    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges


The following object is masked from ‘package:Biostrings’:


    type


The following objects are masked from ‘package:base’:


    aperm, apply



Warning messages:

1: no function found corresponding to methods exports from ‘XVector’ for: ‘concatenateObjects’ 

2: replacing previous import ‘BiocGenerics::dims’ by ‘Biobase::dims’ when loading ‘SummarizedExperiment’ 

3: replacing previous import ‘Biobase::dims’ by ‘DelayedArray::dims’ when loading ‘SummarizedExperiment’ 

4: replacing previous import ‘BiocGenerics::dims’ by ‘Biobase::dims’ when loading ‘ShortRead’ 

5: replacing previous import ‘BiocGenerics::dims’ by ‘Biobase::dims’ when loading ‘AnnotationDbi’ 

6: replacing previous import ‘Biobase::dims’ by ‘BiocGenerics::dims’ when loading ‘AnnotationForge’ 

> 

> targets <- read.delim("targetsPE_chip.txt")

> targets[1:4,-c(5,6)]

           FileName1          FileName2 SampleName Factor

1  BN.H4.1_1.fastq.gz  BN.H4.1_2.fastq.gz     BN.H4.1    BNH4

2  BN.H4.2_1.fastq.gz  BN.H4.2_2.fastq.gz     BN.H4.2    BNH4

3 BN.INPUT_1.fastq.gz BN.INPUT_2.fastq.gz        BN.I     BNI

4 AN.H4.1_1.fastq.gz AN.H4.1_2.fastq.gz    AN.H4.1   ANH4

> args <- systemArgs(sysma="param/trimPE.param", mytargets="targetsPE_chip.txt")

> filterFct <- function(fq, cutoff=20, Nexceptions=0) {

+      qcount <- rowSums(as(quality(fq), "matrix") <= cutoff)

+      fq[qcount <= Nexceptions] # Retains reads where Phred scores are >= cutoff with N exceptions

+  }

> preprocessReads(args=args, Fct="filterFct(fq, cutoff=20, Nexceptions=0)", batchsize=100000)

Error: logical subscript contains NAs

> writeTargetsout(x=args, file="targets_chip_trim.txt", overwrite=TRUE)

Written content of 'targetsout(x)' to file: targets_chip_trim.txt 

> q()

[user@login chipseq]$ cat param/trimPE.param

## Parameter file for read preprocessing

## This is a dummy file to support within the systemPipeR workflow 

## R-based functions that read from input files and write to output files 

## Values in <...> reference column titles in targets file

## PairSet 'type' row specifies whether sofware is commandline (system=TRUE) or R (system=FALSE). If line is ommited 'commandline' will be used

PairSet Name Value

type system FALSE

modules

software NA trim

cores -p 40

other NA

outfile1 -o <FileName1>

outfile1 path ./results/

outfile1 remove .gz

outfile1 append _trim.gz

outfile1 outextension _trim.gz

outfile2 -o <FileName2>

outfile2 path ./results/

outfile2 remove .gz

outfile2 append _trim.gz

outfile2 outextension _trim.gz

reference NA NA

infile1 NA <FileName1>

infile1 path NA

infile2 NA <FileName2>

infile2 path NA

[user@login chipseq]$ cat targetsPE_chip.txt

FileName1 FileName2 SampleName Factor

BN.H4.1_1.fastq.gz BN.H4.1_2.fastq.gz BN.H4.1 BH4

BN.H4.2_1.fastq.gz BN.H4.2_2.fastq.gz BN.H4.2 BH4

BN.INPUT_1.fastq.gz BN.INPUT_2.fastq.gz BN.I BI

AN.H4.1_1.fastq.gz AN.H4.1_2.fastq.gz AN.H4.1 ANH4

AN.H4.2_1.fastq.gz AN.H4.2_2.fastq.gz AN.H4.2 ANH4

AN.INPUT_1.fastq.gz AN.INPUT_2.fastq.gz AN.I ANI

I've tried everything that I can think of but I can't figure out why I keep getting this error. 

Thanks a million